Mg(2+) ions: do they bind to nucleobase nitrogens?

Given the many roles proposed for Mg(2+) in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg(2+) 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(2+) coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg(2+) assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na(+), K(+), NH(4)(+) ions, water molecules or spurious density peaks. Consequently, apart from few documented exceptions, Mg(2+) ions do not bind to N7 atoms. Without much of a surprise, Mn(2+), Zn(2+) and Cd(2+), 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(2+) ribosomal binding site involving two purine N7 atoms. Further, we provide a set of guidelines to help in the assignment of Mg(2+) in crystallographic, cryo-EM, NMR and model building practices and discuss implications of our findings related to ion substitution experiments.