Deflating the RNA Mg²⁺ bubble: stereochemistry to the rescue!

Proper evaluation of the ionic structure of biomolecular systems through X-ray and cryo-EM techniques remains challenging but is essential for advancing our understanding of the underlying structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg²⁺ in deposited structures due to assignment errors finding their origin in improper consideration of stereochemical rules. Herein, to tackle such issues, we reevaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure. We establish that stereochemical principles need to be carefully pondered when examining ion binding features, even when K⁺ anomalous signals are available as is the case for the 6QNR PDB entry. For ribosomes, assignment errors can result in misleading conceptions of their solvent structure. For instance, present stereochemical analysis results in a significant decrease of the number of assigned Mg²⁺ in 6QNR, suggesting that K⁺ and not Mg²⁺ is the prevalent ion in the ribosome first solvation shell. We stress that the use of proper stereochemical guidelines in combination or not with other identification techniques, such as those pertaining to the detection of transition metals, of some anions and of K⁺ anomalous signals, is critical for deflating the current Mg²⁺ bubble witnessed in many ribosome and other RNA structures. We also stress that for the identification of lighter ions such as Mg²⁺, Na⁺, …, for which no anomalous signals can be detected, stereochemistry coupled with high resolution structures (<2.4 Å) remains the best currently available option.