Deflating the RNA Mg²⁺ bubble: stereochemistry to the rescue!

Mg²⁺ and K⁺ coordination distances to oxygen atoms as observed in 4V6F, 6QNR, and the CSD. (A) The red, green, and blue curves show the number of Mg²⁺ and K⁺ bound to rRNA and r-protein oxygen atoms in the 4V6F (Jenner et al. 2010) and 6QNR (Rozov et al. 2019) structures. Water oxygens are excluded. The colored areas and the green and blue dashed lines highlight two regions where Mg²⁺ (1.9–2.4 Å; favored: 2.06 Å) and K⁺ (2.6–3.2 Å; favored: 2.8 Å) should be present. The large second peak in the green curve (≈4.6 Å) appears in a region where a precise ion assignment is problematic since it could correspond to the second coordination shell of Mg²⁺ or to other solvent molecules, including K⁺. (B) Cambridge Structural Database (CSD; Taylor and Wood 2019) histograms showing the Mg²⁺…H₂O (green) and K⁺…O (cyan) coordination distances, the second coordination shell for K⁺ and a H₂O “exclusion zone” for Mg²⁺, where no oxygen atom is expected (gray areas). (C) Schematic representation of the 2.1 and 2.8 Å average coordination distances and 1.9–2.4 and 2.6–3.2 Å coordination range for Mg²⁺ and K⁺, respectively (see panel B). The white area between the green and blue segments (2.4–2.6 Å range) points to improper coordination distance regions for both Mg²⁺ and K⁺. (D) View of the Mg²⁺ assigned in the 4V6F decoding center (Rozov et al. 2016). An examination of the ion coordination features suggests that this ion cannot be Mg²⁺ but is K⁺ as assigned in 6QNR (Rozov et al. 2019) and by us in 5E81 (Leonarski et al. 2019). Density patterns for 6QNR and 5E81 are shown in Supplemental Figure S1.