Carboxylate cluster Mg(II) binding sites consist of a cluster of side-chain carboxylates, typically 3-4 in number, partially buried in a shallow cleft on the surface of a Mg(II) binding protein. Such clusters are often found in the active sites of enzymes catalyzing phosphochemistry. An example is the phospho-signaling protein CheY of the Escherichia coli chemotaxis pathway, which binds Mg(II) via a cluster of three carboxylates at its phosphorylation site. The present study quantitates both the ion charge and size specificity of the CheY site by measuring the dissociation constants of metal ions from groups Ia, IIa, IIIa, and the lanthanides; these spherical cations provide a range of substrates with incrementally varying charge and radius. The site binds divalent and trivalent cations, but it effectively excludes monovalent cations, including the physiological ions Na(I) and K(I). This charge specificity is in contrast to the site's remarkable lack of size specificity: divalent and trivalent cations exhibit affinities which are essentially independent of radius. It is revealing to compare the ion specificity of the Mg(II) site with the previously characterized specificity of the EF-hand class of Ca(II) sites commonly found in Ca(II) signaling proteins. The Mg(II) and Ca(II) sites exhibit similar charge selectivity, but the Ca(II) site is highly size-selective, preferring divalent and trivalent ions with radii similar to that of Ca(II).(ABSTRACT TRUNCATED AT 250 WORDS)