Mg2+ ions: do they bind to nucleobase nitrogens?

ABSTRACT: Given the many roles proposed for Mg²⁺ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg²⁺ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for divalent metals. Further, Mg²⁺ coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg²⁺ assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na⁺, K⁺, NH₄⁺ ions, water molecules or spurious density peaks. Consequently, apart from few documented exceptions, Mg²⁺ ions

SUBMITTER: Leonarski F 

PROVIDER: S-EPMC5314772 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature