Ion report: 6SJ6

date: 2020-04-09 12:50

Authors: Filip Leonarski and Pascal Auffinger
*** beta version: unpublished ***
-> reference 1: Leonarski F., D'Ascenzo L., Auffinger P. (2017) NAR, 45, 987-1004
-> reference 2: Leonarski F., D'Ascenzo L., Auffinger P. (2019) RNA, 25, 173-192

Density maps not assigned - No density checks made in the current version!

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Table of content (ToC):

1) Number of ions of each type and coordination distance ranges used for validation
2) Ion validation table
3) Potential issue list
4) Ion/ligand tables
5) Sorted coded contact list
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REMARKS:
- 1^st shell: correct distance range for coordinating atoms;
- Exclusion zone (excl. zone): a distance range where *no* coordinating atoms should be present;
- Currently coordination distances with sulfur (S) atoms are not considered --> no CD/ZN (cadmium/zinc) validation;
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1) Number of ions of each categorie and coordination distance ranges used for validation

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Ion type	Number	Ion list	Short excl. zone [Angs]	1^st shell [Angs.]	Long excl. zone [Angs]
Sodium (NA)	---		<2.4	2.4 - 2.6	2.6 - 3.6
Potassium (K)	3	A:3057 A:3058 A:3059	<2.6	2.6 - 3.4	---
Caesium (CS)	---		<2.9	2.9 - 3.6	---
Magnesium (MG)	56	A:3001 A:3002 A:3003 A:3004 A:3005 A:3006 A:3007 A:3008 A:3009 A:3010 A:3011 A:3012 A:3013 A:3014 A:3015 A:3016 A:3017 A:3018 A:3019 A:3020 A:3021 A:3022 A:3023 A:3024 A:3025 A:3026 A:3027 A:3028 A:3029 A:3030 A:3031 A:3032 A:3033 A:3034 A:3035 A:3036 A:3037 A:3038 A:3039 A:3040 A:3041 A:3042 A:3043 A:3044 A:3045 A:3046 A:3047 A:3048 A:3049 A:3050 A:3051 A:3052 A:3053 A:3054 A:3055 A:3056	<1.8	1.8 - 2.4	2.4 - 3.4
Calcium (CA)	---		<2.2	2.2 - 2.8	2.8 - 3.6
Strontium (SR)	---		<2.4	2.4 - 2.8	2.8 - 4.0
Barium (BA)	---		<2.6	2.6 - 3.2	---
Manganese (MN)	---		<2.0	2.0 - 2.3	2.3 - 3.6
Zinc (ZN)	---		<1.9	1.9 - 2.3	2.3 - 3.4
Cadmium (CD)	---		<2.2	2.2 - 2.5	2.5 - 3.6
Cobalt (CO)	---		<1.9	1.9 - 2.3	2.3 - 3.5
Iridium (IRI)	---		<2.0	2.0 - 2.3	2.3 - 3.6
Anion (Anion)	---		<2.8	2.8 - 3.4	---
Chloride (CL)	---		<2.8	2.8 - 3.4	---
Sulphate (SO4)	---		<2.8	2.8 - 3.4	---
Phosphate (PO4)	---		<2.8	2.8 - 3.4	---
Total	59

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2) Ion validation table

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NOTES:

- O_ph: OP1 or OP2 anionic phosphate oxygens;
- O_r: O2', O3', O4' or O5' hydroxyl and ester oxygens;
- O_b: O2, O4 or O6 carbonyl oxygens ;
- N_b: N1_A, N3_C, N3_G, N3_A or N7 non-protonated nitrogens;
- O_back: protein backbone carbonyl group;
- O_coo: ASP/GLU carboxyl group;
- O_cno: ASN/GLN carbonyl group;
- OH_Prot: SER/THR/TYR hydroxyl group;
- O_w: water molecule oxygen;
- Anion: NH group (imino, amino and amonium groups) - suggests potential anion contact or poor binding site modeling;

"Large octahedral discrepancy" means a cumulated ligand-ion-ligand angle deviation > 10 deg.;
-> the ions that are currently checked for octahedral coordination are Mg²⁺, Mn²⁺ and Na⁺;
-> could be a hint to the presence of a polyatomic ligand instead of a monoatomic ion;
1^st coordination shell missing:
1) if Mg²⁺ or Na⁺, consider adding a hydration shell and optimize the water to solute distances;
2) if preceding step is not conclusive, consider the presence of another solvent molecule (check crystallisation conditions);
Exclusion atoms:
-> if O3'-O5' atoms are mentioned, this points to a defficient modelling of the RNA backbone;

Ion	Occup.	B-factor	Ligands (1^st shell)	Ligands (excl. zone)	Contacts & potential issues
MG:A:3001	1.00	26.13	1	1	O_ph - Exclusion zone contact(s): /OP1/
MG:A:3002	1.00	2.25	0		1^st MG coordination shell missing (see Notes)
MG:A:3003	1.00	26.13	0	2	- Exclusion zone contact(s): /OP2/OP2/ Consider NA in place of MG (1 valid contact(s) for NA vs. 0 for MG)
MG:A:3004	1.00	26.13	0		1^st MG coordination shell missing (see Notes)
MG:A:3005	1.00	7.17	0	2	- Exclusion zone contact(s): /N7/OP1/ Consider K in place of MG (2 valid contact(s) for K vs. 0 for MG)
MG:A:3006	1.00	26.13	3		3O_ph
MG:A:3007	1.00	8.87	1		O_ph
MG:A:3008	1.00	28.38	1		O_ph
MG:A:3009	1.00	11.52	0		1^st MG coordination shell missing (see Notes)
MG:A:3010	1.00	26.13	1	1	N_b - Exclusion zone contact(s): /OP2/
MG:A:3011	1.00	10.95	0	1	- Exclusion zone contact(s): /OP1/ Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)
MG:A:3012	1.00	26.13	2	1	O_phO_b - Exclusion zone contact(s): /OP1/
MG:A:3013	1.00	26.13	0	2	- Exclusion zone contact(s): /O2'/OP1/ Consider K in place of MG (2 valid contact(s) for K vs. 0 for MG)
MG:A:3014	1.00	15.03	0	1	- Exclusion zone contact(s): /OP2/ Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)
MG:A:3015	1.00	11.75	0		1^st MG coordination shell missing (see Notes)
MG:A:3016	1.00	26.13	0		1^st MG coordination shell missing (see Notes)
MG:A:3017	1.00	26.13	1	2	O_b - Exclusion zone contact(s): /N7/OP2/
MG:A:3018	1.00	14.00	1	2	O_ph - Exclusion zone contact(s): /O5'/OP2/
MG:A:3019	1.00	26.13	1		O_ph
MG:A:3020	1.00	26.13	0	2	- Exclusion zone contact(s): /N7/OP2/ Consider NA in place of MG (1 valid contact(s) for NA vs. 0 for MG)
MG:A:3021	1.00	26.13	1		O_ph
MG:A:3022	1.00	30.82	0		1^st MG coordination shell missing (see Notes)
MG:A:3023	1.00	26.13	1	1	O_ph - Exclusion zone contact(s): /OP2/
MG:A:3024	1.00	28.53	0		1^st MG coordination shell missing (see Notes)
MG:A:3025	1.00	26.13	1		O_ph
MG:A:3026	1.00	8.03	1	1	O_ph - Exclusion zone contact(s): /OP1/
MG:A:3027	1.00	12.04	0	1	- Exclusion zone contact(s): /N7/ Consider NA in place of MG (1 valid contact(s) for NA vs. 0 for MG)
MG:A:3028	1.00	18.26	0		1^st MG coordination shell missing (see Notes)
MG:A:3029	1.00	26.13	0		1^st MG coordination shell missing (see Notes)
MG:A:3030	1.00	26.13	1	1	O_ph - Exclusion zone contact(s): /OP2/
MG:A:3031	1.00	15.90	0	1	- Exclusion zone contact(s): /OP2/ Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)
MG:A:3032	1.00	22.68	1		O_b
MG:A:3033	1.00	13.65	1	1	O_r - Exclusion zone contact(s): /O2/
MG:A:3034	1.00	26.13	0	1	- Exclusion zone contact(s): /N1_A/ Consider NA in place of MG (1 valid contact(s) for NA vs. 0 for MG)
MG:A:3035	1.00	13.93	0	2	- Exclusion zone contact(s): /O4/OP2/ Consider K in place of MG (2 valid contact(s) for K vs. 0 for MG)
MG:A:3036	1.00	13.32	0		1^st MG coordination shell missing (see Notes)
MG:A:3037	1.00	6.73	0		1^st MG coordination shell missing (see Notes)
MG:A:3038	1.00	13.51	1		O_ph
MG:A:3039	1.00	26.13	0	1	- Exclusion zone contact(s): /OP1/ Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)
MG:A:3040	1.00	26.13	0	1	- Exclusion zone contact(s): /O6/ Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)
MG:A:3041	1.00	26.13	0		1^st MG coordination shell missing (see Notes)
MG:A:3042	1.00	14.14	0		1^st MG coordination shell missing (see Notes)
MG:A:3043	1.00	26.13	0	2	- Exclusion zone contact(s): /OP1/OP2/ Consider K in place of MG (2 valid contact(s) for K vs. 0 for MG)
MG:A:3044	1.00	12.14	1	1	O_ph - Exclusion zone contact(s): /OP2/
MG:A:3045	1.00	11.01	1		O_ph
MG:A:3046	1.00	14.10	0	1	- Exclusion zone contact(s): /OP2/ Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)
MG:A:3047	1.00	16.96	1		O_ph
MG:A:3048	1.00	26.13	1		O_ph
MG:A:3049	1.00	26.13	1		O_ph
MG:A:3050	1.00	10.36	1		O_ph
MG:A:3051	1.00	26.13	1		O_ph
MG:A:3052	1.00	17.62	1	1	O_ph - Exclusion zone contact(s): /OP2/
MG:A:3053	1.00	13.79	0	2	- Exclusion zone contact(s): /O2'/O2'/ Consider K in place of MG (2 valid contact(s) for K vs. 0 for MG)
MG:A:3054	1.00	18.51	0	1	- Exclusion zone contact(s): /OP1/ Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)
MG:A:3055	1.00	26.13	0	1	- Exclusion zone contact(s): /OP1/ Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)
MG:A:3056	1.00	30.00	0		1^st MG coordination shell missing (see Notes)
K:A:3057	1.00	26.13	2		2O_ph
K:A:3058	1.00	9.19	0		1^st K coordination shell missing (see Notes)
K:A:3059	1.00	26.13	1		O_ph

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3) Potential issue list

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Problem	Number	Affected ions
1) MG: could be K	13	A:3005 A:3011 A:3013 A:3014 A:3031 A:3035 A:3039 A:3040 A:3043 A:3046 A:3053 A:3054 A:3055
1) MG: could be NA	4	A:3003 A:3020 A:3027 A:3034
2) K: 1^st shell missing	1	A:3058
2) MG: 1^st shell missing	14	A:3002 A:3004 A:3009 A:3015 A:3016 A:3022 A:3024 A:3028 A:3029 A:3036 A:3037 A:3041 A:3042 A:3056
3) K/OP1 contacts	1	A:3057
3) K/OP2 contacts	2	A:3057 A:3059
3) MG/N7 contacts	1	A:3010
3) MG/O2' contacts	1	A:3033
3) MG/O4 contacts	1	A:3032
3) MG/O6 contacts	2	A:3012 A:3017
3) MG/OP1 contacts	10	A:3001 A:3006 A:3006 A:3012 A:3023 A:3025 A:3026 A:3038 A:3047 A:3048
3) MG/OP2 contacts	13	A:3006 A:3007 A:3008 A:3018 A:3019 A:3021 A:3030 A:3044 A:3045 A:3049 A:3050 A:3051 A:3052
3) MG/N1_A excl. contacts	1	A:3034
3) MG/N7 excl. contacts	4	A:3005 A:3017 A:3020 A:3027
3) MG/O2 excl. contacts	1	A:3033
3) MG/O2' excl. contacts	3	A:3013 A:3053 A:3053
3) MG/O4 excl. contacts	1	A:3035
3) MG/O5' excl. contacts	1	A:3018
3) MG/O6 excl. contacts	1	A:3040
3) MG/OP1 excl. contacts	10	A:3001 A:3005 A:3011 A:3012 A:3013 A:3026 A:3039 A:3043 A:3054 A:3055
3) MG/OP2 excl. contacts	15	A:3003 A:3003 A:3010 A:3014 A:3017 A:3018 A:3020 A:3023 A:3030 A:3031 A:3035 A:3043 A:3044 A:3046 A:3052

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4) Ion/ligand tables: all contacts up to 5.0 Angs. are listed

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MG:A:3001

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	OP1	A:1288	2.02	1.00	10.58
2	U	OP1	A:1287	3.12	1.00	13.61
3	U	O3'	A:1287	3.54	1.00	13.61
4	G	OP2	A:1288	4.22	1.00	10.58
5	G	OP2	A:628	4.23	1.00	12.49
6	A	OP2	A:629	4.38	1.00	9.12
7	G	O5'	A:1288	4.41	1.00	10.58
8	A	N1	A:1289	4.58	1.00	9.93
9	U	O5'	A:1287	4.83	1.00	13.61
10	G	O3'	A:1286	4.86	1.00	13.83
11	U	N3	A:856	4.90	1.00	9.98
12	U	O4	A:856	4.94	1.00	9.98

Contact(s): /OP1/
Coded contact list: O_ph
Exclusion zone contact(s): /OP1/

MG:A:3002

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	2.25
1	G	O6	A:520	4.62	1.00	14.65
2	U	OP2	A:29	4.65	1.00	11.39
3	G	O6	A:30	4.74	1.00	13.86
4	U	O4	A:29	4.94	1.00	11.39
5	A	O5'	A:493	4.96	1.00	13.30

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3003

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	OP2	A:2084	2.51	1.00	11.67
2	G	OP2	A:2083	2.61	1.00	11.17
3	G	OP1	A:2083	3.84	1.00	11.17
4	G	OP1	A:2532	4.19	1.00	15.85
5	G	O5'	A:2083	4.19	1.00	11.17
6	G	N7	A:2084	4.32	1.00	11.67
7	G	O5'	A:2084	4.41	1.00	11.67
8	G	OP1	A:2084	4.55	1.00	11.67
9	A	N6	A:2085	4.96	1.00	11.44
10	A	N7	A:2085	4.99	1.00	11.44

Coded contact list:
Exclusion zone contact(s): /OP2/OP2/
Consider NA in place of MG (1 valid contact(s) for NA vs. 0 for MG)

MG:A:3004

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	C	OP1	A:988	3.96	1.00	9.74
2	A	N7	A:989	4.08	1.00	22.70
3	G	OP1	A:876	4.31	1.00	15.65
4	A	N6	A:2475	4.46	1.00	23.61
5	C	OP2	A:988	4.50	1.00	9.74
6	A	N1	A:2475	4.58	1.00	23.61
7	U	OP1	A:611	4.65	1.00	26.13

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3005

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	7.17
1	U	OP1	A:610	2.87	1.00	28.90
2	G	N7	A:854	3.36	1.00	7.77
3	G	OP2	A:853	4.35	1.00	8.21
4	G	N7	A:853	4.49	1.00	8.21
5	G	OP2	A:854	4.51	1.00	7.77
6	U	O5'	A:610	4.54	1.00	28.90
7	U	O3'	A:609	4.64	1.00	20.17
8	G	O5'	A:853	4.78	1.00	8.21
9	G	O6	A:854	4.80	1.00	7.77
10	U	O4	A:855	4.80	1.00	7.93

Coded contact list:
Exclusion zone contact(s): /N7/OP1/
Consider K in place of MG (2 valid contact(s) for K vs. 0 for MG)

MG:A:3006

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	C	OP2	A:1352	1.90	1.00	25.69
2	G	OP1	A:1369	1.96	1.00	15.52
3	C	OP1	A:1351	2.32	1.00	18.81
4	C	OP1	A:1352	3.74	1.00	25.69
5	G	O5'	A:1369	3.77	1.00	15.52
6	C	O3'	A:1351	4.20	1.00	18.81
7	C	O5'	A:1352	4.28	1.00	25.69
8	G	OP2	A:1369	4.30	1.00	15.52
9	C	O3'	A:1368	4.32	1.00	14.91
10	C	OP2	A:1351	4.37	1.00	18.81
11	C	O5'	A:1351	4.39	1.00	18.81
12	U	O3'	A:1350	4.81	1.00	16.36
13	G	O4'	A:1369	4.82	1.00	15.52

1^st shell ligand angles:
1-2: 156; 1-3: 85; 2-3: 108;

Contact(s): /OP1/OP1/OP2/
Coded contact list: 3O_ph

MG:A:3007

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	8.87
1	G	OP2	A:2056	2.18	1.00	13.91
2	G	O5'	A:2056	4.11	1.00	13.91
3	G	OP1	A:2056	4.42	1.00	13.91
4	U	OP1	A:2055	4.54	1.00	12.57
5	U	O5'	A:2055	4.57	1.00	12.57
6	U	O3'	A:2055	4.65	1.00	12.57
7	G	N7	A:2056	4.66	1.00	13.91
8	U	OP2	A:2055	4.99	1.00	12.57

Contact(s): /OP2/
Coded contact list: O_ph

MG:A:3008

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	28.38
1	U	OP2	A:2518	2.00	1.00	24.07
2	G	OP2	A:2482	3.46	1.00	19.37
3	G	OP1	A:2481	3.99	1.00	22.73
4	G	O3'	A:2517	4.08	1.00	22.05
5	U	OP1	A:2518	4.12	1.00	24.07
6	U	O5'	A:2518	4.45	1.00	24.07
7	G	O2'	A:2517	4.46	1.00	22.05
8	G	OP1	A:2482	4.62	1.00	19.37
9	U	OP1	A:2598	4.90	1.00	17.75

Contact(s): /OP2/
Coded contact list: O_ph

MG:A:3009

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	11.52
1	G	N7	A:2521	3.62	1.00	15.89
2	G	O6	A:2521	3.88	1.00	15.89
3	G	O6	A:2522	4.15	1.00	13.74

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3010

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	N7	A:2522	2.17	1.00	13.74
2	G	OP2	A:2522	3.18	1.00	13.74
3	G	O5'	A:2522	3.97	1.00	13.74
4	G	N7	A:2521	3.98	1.00	15.89
5	G	N9	A:2522	4.07	1.00	13.74
6	G	O6	A:2522	4.20	1.00	13.74
7	G	N9	A:2521	4.25	1.00	15.89
8	C	N4	A:2523	4.52	1.00	15.90
9	G	O3'	A:2521	4.66	1.00	15.89

Contact(s): /N7/
Coded contact list: N_b
Exclusion zone contact(s): /OP2/

MG:A:3011

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	10.95
1	U	OP1	A:1007	2.82	1.00	15.13
2	C	OP1	A:2525	3.81	1.00	26.13
3	U	O5'	A:1007	4.49	1.00	15.13
4	A	OP1	A:2524	4.77	1.00	20.05
5	U	OP2	A:1007	4.79	1.00	15.13

Coded contact list:
Exclusion zone contact(s): /OP1/
Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)

MG:A:3012

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	O6	A:613	2.18	1.00	29.41
2	A	OP1	A:2475	2.31	1.00	23.61
3	C	OP1	A:2526	2.72	1.00	21.22
4	A	OP2	A:2475	3.79	1.00	23.61
5	A	O5'	A:2475	3.80	1.00	23.61
6	U	O4	A:612	3.84	1.00	26.13
7	G	N1	A:613	4.07	1.00	29.41
8	U	O2'	A:611	4.60	1.00	26.13
9	C	O3'	A:2525	4.70	1.00	26.13
10	G	O3'	A:2474	4.80	1.00	17.04
11	G	N7	A:613	4.90	1.00	29.41
12	C	OP2	A:2526	4.98	1.00	21.22

1^st shell ligand angles:
1-2: 142;

Contact(s): /O6/OP1/
Coded contact list: O_phO_b
Exclusion zone contact(s): /OP1/

MG:A:3013

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	A	OP1	A:618	2.70	1.00	26.13
2	A	O2'	A:2057	3.16	1.00	23.16
3	U	O2	A:614	3.43	1.00	27.44
4	A	OP2	A:618	3.59	1.00	26.13
5	C	O2'	A:2526	3.72	1.00	21.22
6	A	N3	A:2057	3.81	1.00	23.16
7	G	O2'	A:616	3.96	1.00	14.53
8	U	N3	A:614	4.50	1.00	27.44
9	G	N3	A:616	4.57	1.00	14.53
10	C	O3'	A:2526	4.64	1.00	21.22
11	A	N9	A:2057	4.68	1.00	23.16
12	A	O5'	A:618	4.69	1.00	26.13
13	A	O3'	A:617	4.79	1.00	10.35
14	A	O4'	A:618	4.91	1.00	26.13

Coded contact list:
Exclusion zone contact(s): /O2'/OP1/
Consider K in place of MG (2 valid contact(s) for K vs. 0 for MG)

MG:A:3014

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	15.03
1	A	OP2	A:621	2.73	1.00	10.53
2	G	OP2	A:620	3.61	1.00	14.12
3	A	O5'	A:621	4.57	1.00	10.53
4	C	OP1	A:2044	4.61	1.00	13.78
5	G	O5'	A:620	4.76	1.00	14.12
6	A	OP1	A:2045	4.77	1.00	11.38
7	A	N7	A:621	4.80	1.00	10.53
8	G	O3'	A:620	4.90	1.00	14.12
9	A	OP2	A:2045	4.96	1.00	11.38
10	G	OP1	A:620	5.00	1.00	14.12

Coded contact list:
Exclusion zone contact(s): /OP2/
Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)

MG:A:3015

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	11.75
1	A	OP1	A:1017	4.12	1.00	11.69
2	G	OP1	A:613	4.16	1.00	29.41
3	G	OP2	A:613	4.47	1.00	29.41
4	A	OP2	A:1017	4.53	1.00	11.69
5	G	O2'	A:1016	4.61	1.00	10.51
6	U	OP2	A:612	4.83	1.00	26.13
7	G	O3'	A:1016	4.86	1.00	10.51
8	A	N6	A:865	4.88	1.00	7.60
9	A	N1	A:866	4.94	1.00	9.85

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3016

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	ASN	ND2	U:81	4.19	1.00	18.92
2	U	OP1	A:609	4.23	1.00	20.17
3	C	O3'	A:608	4.28	1.00	14.73
4	U	OP2	A:855	4.44	1.00	7.93
5	U	OP1	A:856	4.44	1.00	9.98
6	C	O2'	A:608	4.84	1.00	14.73

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3017

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	O6	A:1226	2.04	1.00	10.30
2	G	OP2	A:863	2.51	1.00	8.12
3	G	N7	A:1226	3.39	1.00	10.30
4	G	N7	A:863	3.86	1.00	8.12
5	G	N1	A:1226	4.24	1.00	10.30
6	G	O5'	A:863	4.39	1.00	8.12
7	C	OP2	A:862	4.45	1.00	9.46
8	G	OP2	A:1225	4.48	1.00	75.20
9	C	OP1	A:862	4.48	1.00	9.46
10	C	O5'	A:862	4.71	1.00	9.46
11	C	O3'	A:862	4.74	1.00	9.46
12	G	N7	A:1225	4.89	1.00	20.00
13	G	OP1	A:863	4.96	1.00	8.12

Contact(s): /O6/
Coded contact list: O_b
Exclusion zone contact(s): /N7/OP2/

MG:A:3018

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	14.00
1	A	OP2	A:1034	1.99	1.00	12.73
2	C	OP2	A:1035	2.59	1.00	16.47
3	A	O5'	A:1034	3.38	1.00	12.73
4	G	O5'	A:1225	3.75	1.00	78.76
5	U	O3'	A:1224	3.87	1.00	77.17
6	A	OP1	A:1034	3.98	1.00	12.73
7	G	O2'	A:1033	4.20	1.00	13.85
8	U	O5'	A:1224	4.30	1.00	78.76
9	G	O3'	A:1033	4.42	1.00	13.85
10	U	OP1	A:1224	4.58	1.00	78.59
11	C	OP1	A:1035	4.60	1.00	16.47
12	U	OP2	A:1224	4.77	1.00	75.20
13	A	O3'	A:1034	4.89	1.00	12.73
14	C	O5'	A:1035	4.92	1.00	16.47
15	G	O4'	A:1225	4.92	1.00	79.49

Contact(s): /OP2/
Coded contact list: O_ph
Exclusion zone contact(s): /O5'/OP2/

MG:A:3019

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	A	OP2	A:1200	2.13	1.00	13.49
2	A	O5'	A:1199	3.57	1.00	14.20
3	G	O6	A:1201	3.62	1.00	13.84
4	A	OP2	A:1199	3.73	1.00	14.20
5	A	O3'	A:1199	4.28	1.00	14.20
6	A	O5'	A:1200	4.35	1.00	13.49
7	C	N4	A:1042	4.35	1.00	18.00
8	G	O6	A:1041	4.49	1.00	18.23
9	A	OP1	A:1200	4.60	1.00	13.49
10	A	OP1	A:1199	4.62	1.00	14.20

Contact(s): /OP2/
Coded contact list: O_ph

MG:A:3020

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	A	OP2	A:1228	2.42	1.00	7.46
2	G	N7	A:1229	2.61	1.00	9.45
3	G	O6	A:1229	3.68	1.00	9.45
4	GLY	O	O:26	4.33	1.00	26.13
5	A	OP1	A:1228	4.34	1.00	7.46
6	A	O5'	A:1228	4.40	1.00	7.46
7	G	OP2	A:1229	4.66	1.00	9.45
8	G	N2	A:863	4.76	1.00	8.12
9	G	N9	A:1229	4.79	1.00	9.45
10	U	OP1	A:1227	4.80	1.00	9.33
11	U	OP2	A:1227	4.85	1.00	9.33
12	U	O3'	A:1227	4.92	1.00	9.33

Coded contact list:
Exclusion zone contact(s): /N7/OP2/
Consider NA in place of MG (1 valid contact(s) for NA vs. 0 for MG)

MG:A:3021

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	U	OP2	A:987	2.21	1.00	8.73
2	HIS	O	O:35	3.48	1.00	26.13
3	U	OP1	A:987	3.89	1.00	8.73
4	G	OP1	A:877	4.42	1.00	13.07
5	U	O5'	A:987	4.43	1.00	8.73
6	G	O3'	A:986	4.63	1.00	11.15
7	GLY	N	O:37	4.79	1.00	26.13
8	HIS	N	O:35	4.92	1.00	26.13
9	LYS	O	O:36	5.00	1.00	22.86

Contact(s): /OP2/
Coded contact list: O_ph

MG:A:3022

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	30.82
1	C	OP2	A:789	3.56	1.00	12.84
2	HIS	NE2	E:146	4.15	1.00	15.84
3	U	O4	A:791	4.80	1.00	17.70

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3023

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	U	OP1	A:2642	1.96	1.00	10.31
2	A	OP2	A:1303	2.76	1.00	9.47
3	U	O5'	A:2642	3.84	1.00	10.31
4	U	OP2	A:2642	4.19	1.00	10.31
5	A	OP1	A:1303	4.35	1.00	9.47
6	A	O3'	A:2641	4.48	1.00	12.07
7	U	O2'	A:1305	4.59	1.00	8.19
8	G	O3'	A:1302	4.95	1.00	10.87

Contact(s): /OP1/
Coded contact list: O_ph
Exclusion zone contact(s): /OP2/

MG:A:3024

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	28.53
1	G	N7	A:2036	4.30	1.00	10.91
2	U	OP2	A:1305	4.42	1.00	8.19
3	C	N4	A:2035	4.74	1.00	11.37
4	G	O6	A:2036	4.89	1.00	10.91
5	U	OP1	A:1305	4.96	1.00	8.19

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3025

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	U	OP1	A:1305	2.31	1.00	8.19
2	C	OP2	A:2035	4.21	1.00	11.37
3	U	O5'	A:1305	4.36	1.00	8.19
4	U	OP2	A:1305	4.46	1.00	8.19
5	G	O3'	A:1304	4.78	1.00	8.70

Contact(s): /OP1/
Coded contact list: O_ph

MG:A:3026

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	8.03
1	C	OP1	A:2033	1.99	1.00	12.91
2	A	OP1	A:1306	3.07	1.00	6.99
3	A	OP2	A:2076	3.93	1.00	9.58
4	A	O3'	A:2032	3.98	1.00	15.03
5	C	O5'	A:2033	4.14	1.00	12.91
6	G	OP1	A:2075	4.31	1.00	8.20
7	C	OP2	A:2033	4.49	1.00	12.91
8	U	O3'	A:1305	4.57	1.00	8.19

Contact(s): /OP1/
Coded contact list: O_ph
Exclusion zone contact(s): /OP1/

MG:A:3027

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	12.04
1	G	N7	A:2059	2.44	1.00	26.13
2	G	N9	A:2059	3.95	1.00	26.13
3	C	N3	A:2082	3.98	1.00	11.07
4	C	O2	A:2526	4.17	1.00	21.22
5	C	N3	A:2526	4.32	1.00	21.22
6	C	O2	A:2082	4.50	1.00	11.07
7	C	N4	A:2082	4.68	1.00	11.07
8	G	O6	A:2059	4.90	1.00	26.13
9	G	O2'	A:2481	4.94	1.00	22.73

Coded contact list:
Exclusion zone contact(s): /N7/
Consider NA in place of MG (1 valid contact(s) for NA vs. 0 for MG)

MG:A:3028

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	18.26
1	G	O6	A:2054	4.26	1.00	10.81
2	U	O4	A:2053	4.43	1.00	11.87
3	A	OP1	A:2060	4.79	1.00	10.69
4	C	OP2	A:2052	4.89	1.00	11.36

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3029

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	O6	A:2065	3.84	1.00	12.24
2	G	N7	A:2065	4.27	1.00	12.24
3	C	OP2	A:2063	4.30	1.00	9.64
4	A	OP2	A:2064	4.33	1.00	10.88
5	A	N7	A:2064	4.54	1.00	10.88
6	G	O6	A:2066	4.61	1.00	13.82
7	G	OP2	A:575	4.88	1.00	17.81

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3030

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	OP2	A:2529	2.01	1.00	16.97
2	G	OP2	A:2088	2.73	1.00	17.88
3	G	N7	A:2473	3.95	1.00	26.13
4	G	O5'	A:2529	4.26	1.00	16.97
5	G	OP1	A:2529	4.30	1.00	16.97
6	C	O3'	A:2528	4.32	1.00	16.51
7	G	N7	A:2472	4.34	1.00	12.58
8	G	OP2	A:2473	4.42	1.00	26.13
9	A	O2'	A:2087	4.68	1.00	18.70
10	G	O6	A:2473	4.70	1.00	26.13
11	G	OP1	A:2088	4.75	1.00	17.88
12	C	O2'	A:2528	4.77	1.00	16.51
13	A	N3	A:2087	4.80	1.00	18.70
14	A	O3'	A:2087	4.95	1.00	18.70

Contact(s): /OP2/
Coded contact list: O_ph
Exclusion zone contact(s): /OP2/

MG:A:3031

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	15.90
1	A	OP2	A:2089	2.79	1.00	26.13
2	A	OP1	A:2089	3.52	1.00	26.13
3	G	O6	A:2471	3.90	1.00	12.08
4	G	N7	A:2471	3.93	1.00	12.08
5	G	N7	A:2472	4.09	1.00	12.58
6	A	O5'	A:2089	4.50	1.00	26.13
7	G	O6	A:2472	4.53	1.00	12.58
8	G	O3'	A:2088	4.86	1.00	17.88

Coded contact list:
Exclusion zone contact(s): /OP2/
Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)

MG:A:3032

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	22.68
1	U	O4	A:1011	2.26	1.00	22.38
2	G	O6	A:1012	4.03	1.00	19.46
3	G	O6	A:1010	4.11	1.00	21.73
4	G	N7	A:1010	4.29	1.00	21.73
5	U	N3	A:1011	4.49	1.00	22.38
6	A	N6	A:994	4.93	1.00	23.34

Contact(s): /O4/
Coded contact list: O_b

MG:A:3033

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	13.65
1	U	O2'	A:964	2.08	1.00	40.25
2	U	O2	A:964	3.11	1.00	40.25
3	G	O4'	A:965	3.95	1.00	36.02
4	U	N1	A:964	4.07	1.00	40.25
5	U	O4'	A:964	4.32	1.00	40.25
6	C	O2'	B:79	4.79	1.00	58.81
7	U	O3'	A:964	4.81	1.00	40.25
8	A	N1	A:963	4.83	1.00	43.13
9	G	O5'	A:965	4.84	1.00	36.02

Contact(s): /O2'/
Coded contact list: O_r
Exclusion zone contact(s): /O2/

MG:A:3034

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	A	N1	A:963	2.55	1.00	43.13
2	A	N6	A:963	3.44	1.00	43.13
3	A	OP2	A:2295	4.44	1.00	30.94
4	U	O2	A:964	4.47	1.00	40.25
5	A	N3	A:963	4.71	1.00	43.13
6	A	O2'	A:2294	4.94	1.00	23.93

Coded contact list:
Exclusion zone contact(s): /N1_A/
Consider NA in place of MG (1 valid contact(s) for NA vs. 0 for MG)

MG:A:3035

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	13.93
1	C	OP2	A:2275	2.72	1.00	12.78
2	U	O4	A:2276	3.13	1.00	12.04
3	C	OP1	A:2093	3.74	1.00	10.78
4	A	OP1	A:2274	4.45	1.00	13.10
5	C	OP1	A:2275	4.50	1.00	12.78
6	A	O5'	A:2274	4.64	1.00	13.10
7	A	O3'	A:2274	4.89	1.00	13.10
8	A	OP2	A:2274	4.90	1.00	13.10
9	G	OP1	A:2280	4.94	1.00	15.84

Coded contact list:
Exclusion zone contact(s): /O4/OP2/
Consider K in place of MG (2 valid contact(s) for K vs. 0 for MG)

MG:A:3036

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	13.32
1	U	O4	A:2101	4.42	1.00	24.96
2	U	O4	A:2270	4.47	1.00	17.54
3	G	O6	A:2269	4.53	1.00	23.30
4	G	N7	A:2265	4.56	1.00	46.06
5	A	N7	A:2268	4.70	1.00	31.71
6	U	O4	A:2102	4.91	1.00	31.01
7	G	N7	A:2269	4.92	1.00	23.30

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3037

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	6.73
1	G	O6	A:192	3.54	1.00	17.69
2	G	N7	A:208	4.28	1.00	12.20
3	A	N7	A:191	4.43	1.00	18.97
4	G	OP2	A:190	4.52	1.00	18.68
5	A	OP2	A:191	4.93	1.00	18.97

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3038

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	13.51
1	C	OP1	A:31	2.06	1.00	16.62
2	C	OP1	A:1277	3.91	1.00	17.69
3	C	OP2	A:31	4.21	1.00	16.62
4	C	OP1	A:1239	4.26	1.00	13.54
5	G	O3'	A:30	4.35	1.00	13.86
6	C	O5'	A:31	4.40	1.00	16.62
7	C	O3'	A:1277	4.76	1.00	17.69
8	C	O5'	A:1277	4.86	1.00	17.69

Contact(s): /OP1/
Coded contact list: O_ph

MG:A:3039

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	A	OP1	A:1275	2.72	1.00	17.92
2	A	OP2	A:523	4.23	1.00	28.92
3	G	OP1	A:522	4.32	1.00	24.05
4	A	O5'	A:1275	4.65	1.00	17.92
5	G	OP2	A:522	4.74	1.00	24.05

Coded contact list:
Exclusion zone contact(s): /OP1/
Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)

MG:A:3040

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	O6	A:381	3.38	1.00	28.33
2	A	N6	A:343	3.67	1.00	34.48
3	A	N7	A:342	4.15	1.00	35.16
4	A	OP2	A:342	4.16	1.00	35.16
5	G	N7	A:381	4.68	1.00	28.33
6	A	N7	A:343	4.88	1.00	34.48

Coded contact list:
Exclusion zone contact(s): /O6/
Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)

MG:A:3041

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	O6	A:539	4.21	1.00	22.88
2	G	O6	A:538	4.26	1.00	22.76
3	A	OP2	A:537	4.81	1.00	23.88
4	G	N7	A:538	4.82	1.00	22.76

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3042

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	14.14
1	G	N7	A:1329	3.60	1.00	21.90
2	G	O6	A:1329	4.53	1.00	21.90
3	U	O4	A:1330	4.58	1.00	22.68

Coded contact list:
1^st MG coordination shell missing (see Notes)

MG:A:3043

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	C	OP2	A:1334	2.74	1.00	22.45
2	U	OP1	A:1683	3.07	1.00	23.47
3	A	OP1	A:1333	4.07	1.00	21.24
4	C	OP1	A:1334	4.37	1.00	22.45
5	U	OP2	A:1683	4.46	1.00	23.47
6	A	O5'	A:1333	4.50	1.00	21.24
7	G	N2	A:2736	4.53	1.00	22.20
8	G	O2'	A:2736	4.54	1.00	22.20
9	G	N3	A:2736	4.55	1.00	22.20
10	A	OP2	A:1333	4.69	1.00	21.24
11	A	O3'	A:1333	4.72	1.00	21.24

Coded contact list:
Exclusion zone contact(s): /OP1/OP2/
Consider K in place of MG (2 valid contact(s) for K vs. 0 for MG)

MG:A:3044

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	12.14
1	C	OP2	A:1335	2.17	1.00	24.80
2	U	OP2	A:1683	3.17	1.00	23.47
3	G	N7	A:1336	3.78	1.00	26.97
4	G	O6	A:1336	4.04	1.00	26.97
5	U	O5'	A:1683	4.10	1.00	23.47
6	C	O5'	A:1335	4.33	1.00	24.80
7	C	OP1	A:1335	4.39	1.00	24.80
8	C	O3'	A:1334	4.64	1.00	22.45
9	C	O5'	A:1682	4.74	1.00	18.59
10	C	OP2	A:1682	4.76	1.00	18.59
11	C	OP1	A:1682	4.82	1.00	18.59

Contact(s): /OP2/
Coded contact list: O_ph
Exclusion zone contact(s): /OP2/

MG:A:3045

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	11.01
1	U	OP2	A:1680	1.97	1.00	17.96
2	U	O5'	A:1680	3.87	1.00	17.96
3	A	OP1	A:1679	3.92	1.00	21.29
4	U	OP1	A:1680	3.93	1.00	17.96
5	U	OP2	A:1681	4.13	1.00	15.79
6	A	OP1	A:1337	4.26	1.00	32.54
7	A	O3'	A:1679	4.46	1.00	21.29

Contact(s): /OP2/
Coded contact list: O_ph

MG:A:3046

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	14.10
1	A	OP2	A:1786	2.96	1.00	78.59
2	A	N7	A:1787	3.74	1.00	19.95
3	A	N6	A:1787	4.08	1.00	19.95
4	G	O5'	A:1785	4.30	1.00	78.76
5	U	N3	A:1784	4.37	1.00	24.51
6	A	O5'	A:1786	4.38	1.00	78.76
7	U	O4	A:1788	4.47	1.00	21.80
8	U	O4	A:1784	4.64	1.00	24.51
9	U	N1	A:1784	4.65	1.00	24.51
10	A	OP2	A:1787	4.69	1.00	19.95
11	A	N7	A:1786	4.95	1.00	20.00

Coded contact list:
Exclusion zone contact(s): /OP2/
Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)

MG:A:3047

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	16.96
1	A	OP1	A:847	2.22	1.00	14.11
2	G	OP2	A:719	4.22	1.00	10.39
3	A	OP2	A:720	4.30	1.00	11.53
4	A	OP2	A:847	4.40	1.00	14.11
5	A	O5'	A:847	4.52	1.00	14.11
6	G	O3'	A:846	4.53	1.00	17.01
7	U	O4	A:848	4.74	1.00	26.13

Contact(s): /OP1/
Coded contact list: O_ph

MG:A:3048

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	A	OP1	A:845	2.01	1.00	10.91
2	A	OP2	A:845	3.99	1.00	10.91
3	G	O3'	A:844	4.26	1.00	9.13
4	A	O5'	A:845	4.41	1.00	10.91
5	C	N3	A:195	4.51	1.00	8.54
6	A	N7	A:845	4.67	1.00	10.91
7	C	N4	A:195	4.80	1.00	8.54
8	A	N1	A:194	4.87	1.00	9.22

Contact(s): /OP1/
Coded contact list: O_ph

MG:A:3049

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	OP2	A:496	2.16	1.00	8.97
2	G	OP2	A:498	4.10	1.00	9.39
3	GLY	O	F:86	4.20	1.00	27.49
4	G	OP1	A:496	4.27	1.00	8.97
5	G	O5'	A:496	4.34	1.00	8.97
6	A	OP1	A:495	4.61	1.00	12.55
7	A	O3'	A:495	4.63	1.00	12.55
8	GLY	O	F:85	4.77	1.00	26.13
9	A	O5'	A:495	4.94	1.00	12.55

Contact(s): /OP2/
Coded contact list: O_ph

MG:A:3050

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	10.36
1	G	OP2	A:1226	2.33	1.00	10.30
2	C	OP2	A:861	3.53	1.00	9.55
3	G	OP2	A:1225	3.64	1.00	75.20
4	C	OP2	A:862	3.66	1.00	9.46
5	G	OP1	A:1226	4.12	1.00	10.30
6	G	O5'	A:1226	4.14	1.00	10.30
7	U	O2'	A:1224	4.28	1.00	79.34
8	G	OP1	A:1225	4.35	1.00	78.59
9	C	OP1	A:861	4.46	1.00	9.55
10	C	O5'	A:861	4.51	1.00	9.55
11	G	O3'	A:1225	4.82	1.00	77.17
12	G	O6	A:863	4.83	1.00	8.12

Contact(s): /OP2/
Coded contact list: O_ph

MG:A:3051

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	G	OP2	A:1803	2.13	1.00	16.76
2	G	OP1	A:1803	4.05	1.00	16.76
3	G	N7	A:1803	4.13	1.00	16.76
4	A	OP1	A:2008	4.33	1.00	14.73
5	G	O5'	A:1803	4.48	1.00	16.76
6	U	O3'	A:1802	4.49	1.00	17.21

Contact(s): /OP2/
Coded contact list: O_ph

MG:A:3052

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	17.62
1	C	OP2	A:776	2.32	1.00	22.95
2	A	OP2	A:775	2.92	1.00	22.79
3	A	OP1	A:806	3.41	1.00	14.92
4	C	O5'	A:776	4.25	1.00	22.95
5	A	O3'	A:775	4.33	1.00	22.79
6	G	OP1	A:808	4.33	1.00	20.57
7	A	O5'	A:806	4.36	1.00	14.92
8	A	OP2	A:806	4.43	1.00	14.92
9	A	N3	A:775	4.70	1.00	22.79
10	A	O5'	A:775	4.72	1.00	22.79
11	G	O3'	A:774	4.82	1.00	19.97
12	C	OP1	A:776	4.91	1.00	22.95
13	U	OP1	A:807	4.98	1.00	20.69

Contact(s): /OP2/
Coded contact list: O_ph
Exclusion zone contact(s): /OP2/

MG:A:3053

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	13.79
1	A	O2'	A:660	2.81	1.00	31.89
2	U	O2'	A:661	3.22	1.00	30.89
3	ARG	NE	F:106	3.55	1.00	17.14
4	A	O4'	A:660	4.06	1.00	31.89
5	G	OP2	A:662	4.82	1.00	32.03

Coded contact list:
Exclusion zone contact(s): /O2'/O2'/
Consider K in place of MG (2 valid contact(s) for K vs. 0 for MG)

MG:A:3054

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	18.51
1	C	OP1	A:2836	3.33	1.00	25.09
2	LEU	O	4:39	3.59	1.00	48.74
3	C	O3'	A:2835	4.58	1.00	36.85
4	GLU	OE2	Q:115	4.66	1.00	16.11
5	GLU	OE1	Q:115	4.68	1.00	16.11

Coded contact list:
Exclusion zone contact(s): /OP1/
Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)

MG:A:3055

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	C	OP1	A:777	2.64	1.00	22.74
2	G	OP1	A:2007	3.97	1.00	20.17
3	G	OP1	A:805	4.39	1.00	12.56
4	C	OP2	A:777	4.54	1.00	22.74
5	G	OP2	A:805	4.71	1.00	12.56
6	C	O3'	A:776	4.94	1.00	22.95
7	C	O5'	A:777	4.94	1.00	22.74

Coded contact list:
Exclusion zone contact(s): /OP1/
Consider K in place of MG (1 valid contact(s) for K vs. 0 for MG)

MG:A:3056

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	30.00
1	A	OP2	A:2480	3.80	1.00	23.38
2	A	N7	A:2480	4.01	1.00	23.38
3	G	N7	A:2481	4.16	1.00	22.73
4	G	O6	A:2481	4.74	1.00	22.73
5	C	OP2	A:2479	4.75	1.00	26.13

Coded contact list:
1^st MG coordination shell missing (see Notes)

K:A:3057

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	C	OP1	A:1714	2.75	1.00	13.13
2	U	OP2	A:1715	2.78	1.00	14.86
3	G	OP2	A:2577	3.97	1.00	35.40
4	G	OP2	A:2576	4.11	1.00	26.76
5	C	O3'	A:1714	4.51	1.00	13.13
6	U	OP1	A:1715	4.66	1.00	14.86
7	A	O3'	A:1713	4.92	1.00	14.81
8	C	O5'	A:1714	4.92	1.00	13.13

1^st shell ligand angles:
1-2: 75;

Contact(s): /OP1/OP2/
Coded contact list: 2O_ph

K:A:3058

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	9.19
1	G	O6	A:707	4.14	1.00	17.35
2	G	N7	A:707	4.24	1.00	17.35
3	U	O4	A:637	4.51	1.00	17.75
4	A	N6	A:636	4.94	1.00	15.72
5	U	O4	A:709	4.99	1.00	14.86

Coded contact list:
1^st K coordination shell missing (see Notes)

K:A:3059

	Res. type	Atom	Residue	Distance	Occupancy	B-factor
Ion					1.00	26.13
1	A	OP2	A:880	3.19	1.00	14.20
2	G	O6	A:986	4.50	1.00	11.15
3	A	N7	A:880	4.59	1.00	14.20
4	A	O5'	A:880	4.81	1.00	14.20
5	U	OP2	A:879	4.84	1.00	12.68
6	G	O6	A:881	4.96	1.00	14.18
7	U	O5'	A:879	4.96	1.00	12.68

Contact(s): /OP2/
Coded contact list: O_ph
________________________________________________________________

5) Sorted coded contact list

Go to ToC

NOTES:

- N. --> estimate of the coordination number as deduced from the PDB structure;
- Excl. --> existence of contacts in the ligand exclusion zone;
- Bad hyd. --> existence of 2^nd shell hydration contacts shorter than 2.4 Angs.;
- Lines in red mark stereochemical issues that should be addressed;
- Lines in green mark ions without stereochemical issues - Please note that this does not always warrant the quality of the ion identification;

(1) N=0 --> No 1^st shell coordination: impossible to assess ion identity;
(2) Exclusion contacts --> Probable wrong ion identity - poor modelization of the ion binding site is also possible;
(3) Bad 2^nd hydration shell contacts --> Poor modelization of the hydration shell and/or binding site;
(4) Check for anion (Cl^-, ...);
(5) Mixed contacts with unprotonated O/N and protonated N, suggest poorly modeled binding site;
(6) Currently the ZN (Zinc) and CD (Cadmium) coordination is not evaluated;
(7) Check occupancies - partial occupancies are not reliable at medium to low resolutions, especially for solvent particles;
(8) Check B-factors;

Ion	Number	Code	N.	Excl.	Bad hyd.	Notes	Ion list
MG:	17	No 1^st shell	>1	Yes	No	(2)	A:3003 A:3005 A:3011 A:3013 A:3014 A:3020 A:3027 A:3031 A:3034 A:3035 A:3039 A:3040 A:3043 A:3046 A:3053 A:3054 A:3055
MG:	14	No 1^st shell	=0	No	No	(1)	A:3002 A:3004 A:3009 A:3015 A:3016 A:3022 A:3024 A:3028 A:3029 A:3036 A:3037 A:3041 A:3042 A:3056
MG:	12	O_ph	1	No	---		A:3007 A:3008 A:3019 A:3021 A:3025 A:3038 A:3045 A:3047 A:3048 A:3049 A:3050 A:3051
MG:	7	O_ph	>1	Yes	---	(2)	A:3001 A:3018 A:3023 A:3026 A:3030 A:3044 A:3052
MG:	1	N_b	>1	Yes	---	(2)	A:3010
MG:	1	O_r	>1	Yes	---	(2)	A:3033
MG:	1	O_phO_b	>2	Yes	---	(2)	A:3012
K:	1	O_ph	1	No	---		A:3059
K:	1	2O_ph	2	No	---		A:3057
MG:	1	O_b	>1	Yes	---	(2)	A:3017
K:	1	No 1^st shell	=0	No	No	(1)	A:3058
MG:	1	O_b	1	No	---		A:3032
MG:	1	3O_ph	3	No	---		A:3006
							List of ions with partial occupancies
						Total:	0

Total number of Mg²⁺: 56
Total number of Mg²⁺ with stereochemical issues: 41
Total number of Mg²⁺ without stereochemical issues: 15
Total number of K⁺: 3
Total number of K⁺ with stereochemical issues: 1
Total number of K⁺ without stereochemical issues: 2
Total number of Na⁺: 0
Total number of Na⁺ with stereochemical issues: 0
Total number of Na⁺ without stereochemical issues: 0

Ion report: 6SJ6

date: 2020-04-09 12:50

Table of content (ToC):

1) Number of ions of each categorie and coordination distance ranges used for validation

Go to ToC

2) Ion validation table

Go to ToC

3) Potential issue list

Go to ToC

4) Ion/ligand tables: all contacts up to 5.0 Angs. are listed

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MG:A:3001

MG:A:3002

MG:A:3003

MG:A:3004

MG:A:3005

MG:A:3006

MG:A:3007

MG:A:3008

MG:A:3009

MG:A:3010

MG:A:3011

MG:A:3012

MG:A:3013

MG:A:3014

MG:A:3015

MG:A:3016

MG:A:3017

MG:A:3018

MG:A:3019

MG:A:3020

MG:A:3021

MG:A:3022

MG:A:3023

MG:A:3024

MG:A:3025

MG:A:3026

MG:A:3027

MG:A:3028

MG:A:3029

MG:A:3030

MG:A:3031

MG:A:3032

MG:A:3033

MG:A:3034

MG:A:3035

MG:A:3036

MG:A:3037

MG:A:3038

MG:A:3039

MG:A:3040

MG:A:3041

MG:A:3042

MG:A:3043

MG:A:3044

MG:A:3045

MG:A:3046

MG:A:3047

MG:A:3048

MG:A:3049

MG:A:3050

MG:A:3051

MG:A:3052

MG:A:3053

MG:A:3054

MG:A:3055

MG:A:3056

K:A:3057

K:A:3058

K:A:3059

5) Sorted coded contact list

Go to ToC

### END ###