Abstract
Halides are negatively charged ions of halogens, forming fluoride (F-), chloride (Cl-), bromide (Br-) and iodide (I-). These ions are quite reactive and interact both specifically and non-specifically with proteins. In this study we have developed a protocol and a pipeline for the analysis of halide binding sites in proteins. Our analysis revealed that all of halides are strongly attracted by the guanidinium moiety of arginine side chains, however there are also certain preferences among halides for other partners. Furthermore, there is a certain preference for coordination numbers in the binding sites. Taken together now it is possible to assign the identity of bound ion based on the geometry and composition of binding sites and it should be possible to predict halide binding sites in future. This is of use for characterization of specific halideprotein interactions and phasing techniques relying on halides as anomalous scatters.