Stereochemistry of binding of metal cations and water to a phosphate group

Distributions of five metal cations (Na+, Mg2+, K+, Ca2+, Zn2+) and water around a phosphate group with charge -1 compiled from crystal structures showed that these species prefer to bind in sterically well-defined and distinct positions. The differences between the stereochemistry of binding of these metal cations may be related to the different effects they have on thermodynamic properties and conformational equilibria of DNA. All the studied cations prefer asymmetric monodentate positions where they bind to only one of the two charged oxygens (OF) while the bidentate site located symmetrically between the two OP atoms is not occupied at all. Mg2+ and Zn2+ have just one binding site, Na+ has two sites, and K+ and water have three sites. Water distributions from Na+, Mg2+, Zn2+, and Ca2+ phosphate salts resemble each other but they are modified by the distribution of the accompanying metal. The Mg2+ and Zn2+ distributions are spatially most constrained and have the smallest volumes. The distributions of K+ and water have up to eight times and that of Na+ four times larger volume. The cation and water distributions were analyzed from 18(9, 9, 6, 12) crystal structures of Na+ (Mg2+, K+, Ca2+, and Zn2+) salts of organic phosphates (charge -1, R-factor of 10% or better, deposited in the Cambridge Structural Database) by a Fourier averaging technique described elsewhere (Schneider et al: Biophys. J. 1993, 64, 2291).