A molecular dynamics (MD) simulation on the contents of two asymmetric units of the crystal structure of the bacterial serine proteinase, Streptomyces griseus proteinase A (SGPA), resulted in four dihydrogen phosphate anions migrating to form a cluster in a solvent region far removed from the protein surface. In an effort to provide experimental verification for this unexpected phenomenon, native SGPA crystals were soaked in 2·0 M KH2AsO4; intensity data were collected and difference electron density maps examined for evidence of H2AsO-4 ion clusters. These maps did not corroborate the cluster observed in the MD simulation. They did, however, show positive electron density features located in the active site cavity that could be interpreted as a tetrapeptide. Gly-Ala-Ser (β-OH)Asp, covalently bonded to Oγ of Ser195 as an acyl-enzyme intermediate. There was also a peak of electron density corresponding to an ideal position for the hydrolytic water in the deacylation reaction. This density is centred 3·1 AÅ from His57 N2 and 2·7 AÅ from the carbonyl-carbon atom of the planar acyl-ester bond of the complex. The carbonyl-oxygen atom of the ester is located in the oxyanion pocket and participates in hydrogen bonds with Gly193 NH (2·6 AÅ) and Ser195 NH (3·0 AÅ). © 1994 Academic Press Limited.