Imaging

@article{,

title = {Nucleobase carbonyl groups are poor Mg^{2+} inner-sphere binders but excellent monovalent ion binders - A critical PDB survey},

author = {F Leonarski and L D'Ascenzo and P Auffinger},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30409785?dopt=Abstract},

doi = {10.1261/rna.068437.118},

isbn = {30409785},

year  = {2019},

date = {2019-01-01},

journal = {RNA},

volume = {25},

number = {2},

pages = {173-192},

abstract = {Precise knowledge of Mg2+ inner-sphere binding site characteristics is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, that represents the main source of Mg2+ binding sites, contains a significant number of ion assignment issues that significantly blur our understanding of the functions of these ions. Here, following a preceding study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed PDB nucleic acid crystallographic structures with resolutions < 2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether and phosphodiester oxygen atoms to derive a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected given that many of those bind misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide crystallographic evidence that nucleobases are poor inner-sphere Mg2+ binders but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline metal ion stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ should be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.},

keywords = {DNA lanthanides magnesium ribosome ribozyme, ENNIFAR, Unité ARN},

pubstate = {published},

tppubtype = {article}

}