An uncommon [K⁺(Mg²⁺)₂] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch

Guanidine-binding pocket structure. (A) The Burkholderia ykkC-I guanidine-binding pocket, colored as in Figure 1. Gray mesh depicts portion of the |F_o|–|F_c| electron density map, prior to ligand modeling, contoured at 2.0σ. Hydrogen bonds are depicted as black dashed lines. Bound guanidine is shown in yellow ball-and-stick representation. (B) 80° rotation of A. (C) Structural superposition of Burkholderia residues on the corresponding D. dadantii binding pocket (RNA, orange; guanidine, magenta). Residue numbers in parentheses correspond to PDB ID 5U3G (Battaglia et al. 2017). (D) Structural superposition on the S. acidophilus binding pocket (RNA, gray; guanidine, magenta). Residue numbers in parentheses correspond to PDB ID 5T83 (Reiss et al. 2017). Structural superpositions were performed for all non-hydrogen atoms, with residues 20–41 and 63–102 of the Burkholderia RNA omitted. (E) Van der Waals representation of A55 from Burkholderia ykkC-I and G67 from D. dadantii Guanidine-I. (F) Van der Waals representation of A55 from Burkholderia ykkC-I and G72 from S. acidophilus Guanidine-I.