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 do not bind to N7 atoms. Without much of a surprise, Mn²⁺, Zn²⁺ and Cd²⁺, which have a higher affinity for nitrogens, may contact N7 atoms when present in crystallization buffers. In this respect, we describe for the first time a potential Zn²⁺ ribosomal binding site involving two purine N7 atoms. Further, we provide a set of guidelines to help in the assignment of Mg²⁺ in crystallographic, cryo-EM, NMR and model building practices and discuss implications of our findings related to ion substitution experiments.