Abnormally short water to rRNA and r-protein contact distances reveal ill-placed Mg2+ in 6QNR. (A) The red curve shows the number of contacts between water molecules of the Mg2+ first hydration shell and rRNA and r-protein oxygen atoms with respect to distance. The 564 contacts <2.4 Å reveal the presence of ill-placed Mg2+. Note the forgiving 2.4 Å hydrogen bond limit; a hydrogen bond is only exceptionally shorter than 2.5–2.6 Å (Kruse et al. 2019) and is more generally centered around 2.8 Å (gray box). (B) Example of a Mg2+ in 6QNR whose hydration sphere clashes with three oxygen atoms (red dashed lines; see also Supplemental Fig. S3). The 2.75 Å distance to a phosphate oxygen atom suggests the presence of K+ and unambiguously discards that of Mg2+ (green dashed line). Note the average d(Mg2+…Ow) distance close to 2.17 Å. (C) The corresponding 2Fo−Fc map contoured at 1.0 σ level around Mg2+ reveals no clear octahedral coordination pattern (for comparison, see Supplemental Fig. S3).
