Nucleobase carbonyl groups are poor Mg²⁺ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey.

ABSTRACT: Precise knowledge of Mg²⁺ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg²⁺ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg²⁺ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg²⁺ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg²⁺ binding sites. We report that cr

SUBMITTER: Leonarski F 

PROVIDER: S-EPMC6348993 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature