Mg2+ ions: do they bind to nucleobase nitrogens?

Given the many roles proposed for Mg in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg 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, Mg coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na, K, NH ions, water molecules or spurious density peaks. Consequently, apart from few documented exceptions, Mg ions do not bind to N7 atoms. Without much of a surprise, Mn, Zn and Cd, 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 Zn ribosomal binding site involving two purine N7 atoms. Further, we provide a set of guidelines to help in the assignment of Mg in crystallographic, cryo-EM, NMR and model building practices and discuss implications of our findings related to ion substitution experiments.