Principles of ion binding to RNA inferred from the analysis of a 1.55 A resolution bacterial ribosome structure - Part I: Mg2.

ABSTRACT: The importance of Mg2+ ions for RNA structure and function cannot be overstated. Several attempts were made to establish a comprehensive Mg2+ binding site classification. However, such descriptions were hampered by poorly modelled ion binding sites as observed in a recent cryo-EM 1.55 Å Escherichia coli ribosome structure where incomplete ion assignments blurred our understanding of their binding patterns. We revisited this model to establish general binding principles applicable to any RNA of sufficient resolution. These principles rely on the 2.9 Å distance separating two water molecules bound in cis to Mg2+. By applying these rules, we could assign all Mg2+ ions bound with 2-4 non-water oxygens. We also uncovered unanticipated motifs where up to five adjacent nucleotides wrap around a s

SUBMITTER: Leonarski F 

PROVIDER: S-EPMC11724316 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature