ArticleNucleic acids research2025
Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Article
- Comparative assessment of crystallographic and cryo-EM models in the Protein Data Bank.FEBS open bio · 2026Article
- Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models.Nucleic acids research · 2026Article
- Comparative Evaluation of Explicit Solvent Models for RNA-Ligand Docking.Journal of chemical information and modeling · 2026Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- NNature · 2026Article
- Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex.Nucleic acids research · 2025Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.bioRxiv : the preprint server for biology · 2025Article
- Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact?Life (Basel, Switzerland) · 2025Article
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5 authors.
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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 single ion. The formation of such motifs involves a hierarchical Mg2+ ion dehydration process that plays a significant role in ribosome biogenesis and in the folding of large RNAs. Besides, we established a classification of the Mg2+…Mg2+ and Mg2+…K+ ion pairs observed in this ribosome. Overall, the uncovered binding principles enhance our understanding of the roles of ions in RNA structure and will help refining the solvation shell of other RNA systems.
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