Binding of metals to purine N7 nitrogen atoms and implications for nucleic acids: A CSD survey

Abstract

Understanding the structure and function of RNA and DNA systems depends partly on our comprehension of the binding features of metal ions to nucleobases. Such knowledge is important for an unambiguous assignment of ionic species to solvent electronic densities in crystallographic structures. Since the purine N7 atom is considered to be the best nucleobase metal binding site, we focus herein on describing the occurrence and coordination geometries of direct binding of alkali, alkaline earth and biologically relevant transition metals to this site. Further, we compare binding of such metals to purine N7 atoms, as well as imine sites occurring in small molecules such as imidazolates and water molecules. We analyze also the structure of the coordination shell of penta- and tetrahydrated metal ions bound to one or two purine N7 atoms. These structures can be used to validate proposed Mg2+ and other metal binding sites in large PDB structures where such assignments are often difficult to make. This survey suggests that Mg2+ ions bind with weak affinities to nucleobase N7 atoms. Although Mg2+ ions are essential to nucleic acid systems, purine N7 binding sites are, in most contexts, probably not of primary importance in RNA and DNA.