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

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 & Aring; 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 & Aring; 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+& mldr;Mg2+ and Mg2+& mldr;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. Magnesium ions (Mg2+) are crucial for the structure and function of RNA. Researchers have tried to classify how Mg2+ binds to RNA, but this has been difficult due to poorly modeled ion binding sites. A recent study on an E. coli ribosome structure revealed incomplete ion assignments, making it hard to understand their binding patterns. By revisiting this model, the authors established general principles for Mg2+ binding that can be applied to any RNA with sufficient resolution. These principles are based on the distance between two water molecules bound to Mg2+. Using these rules, they identified all Mg2+ ions bound with 2-4 non-water oxygen atoms. They also discovered new binding motifs where up to five nucleotides wrap around a single ion. This process involves a step-by-step dehydration of Mg2+ ions, which is important for ribosome formation and RNA folding. Additionally, they classified pairs of Mg2+ and potassium (K+) ions found in the ribosome. These findings improve our understanding of ion roles in RNA structure and will help refine the solvation shell of other RNA systems.