Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg ²⁺

The importance of Mg ²⁺ ions for RNA structure and function can difficultly be overstated. Several attempts were made to establish a comprehensive Mg ²⁺ binding site classification. However, such descriptions were hampered by poorly modelled ion binding sites. Recently, ribosome cryo-EM structures with resolutions < 2.0 Å allowed more detailed ion binding site descriptions. However, such a task is challenging. In a recent 1.55 Å E. coli ribosome structure (PDBid 8B0X), ion assignment incompleteness/errors were observed that prevent a full understanding of the chelated ion structures. We reinspected this cryo-EM reconstruction by using stereochemical constraints derived from an updated analysis of the Mg ²⁺ /K ⁺ occurrences in the Cambridge Structural Database (CSD) and established sufficiently straightforward and general binding principles to be applicable to any RNA of sufficient resolution. Through our improved characterization of the RNA ionic structure, we assigned all Mg ²⁺ ions bound to 2 up to 4 non-water oxygens leading to a better understanding of the role of Mg ²⁺ ions in folding while shedding light on the importance of Mg ²⁺ …Mg ²⁺ /K ⁺ ion pairs in catalytic systems. Based on these data, we defined general Mg ²⁺ binding rules allowing to describe unanticipated motifs where up to five adjacent nucleotides wrap around a single ion.