Buried chloride stereochemistry in the protein data bank

Abstract

Background: Despite the chloride anion is involved in fundamental biological processes, its interactions with proteins are little known. In particular, we lack a systematic survey of its coordination spheres. Results: The analysis of a non-redundant set (pairwise sequence identity < 30%) of 1739 high resolution (<2 Å) crystal structures that contain at least one chloride anion shows that the first coordination spheres of the chlorides are essentially constituted by hydrogen bond donors. Amongst the side-chains positively charged, arginine interacts with chlorides much more frequently than lysine. Although the most common coordination number is 4, the coordination stereochemistry is closer to the expected geometry when the coordination number is 5, suggesting that this is the coordination number towards which the chlorides tend when they interact with proteins. Conclusions: The results of these analyses are useful in interpreting, describing, and validating new protein crystal structures that contain chloride anions.