Valence screening of water in protein crystals reveals potential Na+ binding sites

Identification of Na+ binding sites in protein crystals is complicated by comparable electron density of this monovalent cation and water. Valence calculations can predict the location of metal ion binding sites in proteins with high precision. These calculations were used to screen 332,242 water molecules in 2742 protein structures reported in the Protein Data Bank (PDB), searching for molecules with Na+/- specific valence values V(Na+) > or = 1.0 v.u., as expected for a bound Na ion. Thirty-three water molecules (<0.01% of the total) were found be have V(Na+) > or = 1.0 v.u. and to be located within 3.5 A from at least two protein oxygen atoms. These water molecules, with a high Na+ -specific valence, do not have valences specific for other cations, like Li+, K+, Mg2+ or Ca2+. They belong to nine different proteins (deoxyribonuclease I, enolase, hen egg-white lysozyme, human lysozyme, phospholipase A2, proteinase A, rubredoxin, thrombin and phage T4 lysozyme) and appear with similar coordination geometry, typically octahedral, in the same place in multiple crystal structure determinations of the same protein. In the case of thrombin, the water molecule singled out by valence calculations is, in fact, a bound Na ion as demonstrated by molecular replacement with Rb+. Valence calculations provide an accurate screening of water in protein crystals and may help identify Na+ binding sites of functional importance.