Additional file 2: of Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD

Chloride binding site. Two examples are shown: TtSlyDFL:S2-W23A chain A (left) and TtSlyDFL:FK506 chain B (right). TtSlyD is white, the peptide is pink, chloride is turquoise, and water molecules are red. The transparent spheres indicate the van der Waal radii of the chloride ions as given by PyMol. Distances up to 3.4 Å (first coordination sphere of chloride [70]) are indicated with black dashes and longer distances are gray. The annotation as chloride was based on the binding mode and the electron density maps (including the anomalous difference Fourier map where weak density for the ion could be recognized). The backbone nitrogen atoms of L30 and A148 interact with the ion. The distance here is ~3.2 Å for all structures, which is the most commonly found coordination distance for chloride [70]. The side chain of N35 also contacts the ion, though the distances here are longer and more variable. When an S2, S2-W23A, or S3 peptide is bound, the Nζ atom of K28S2/K16S3 is within 3.1–3.6 Å of the ion (left panel). The number of ligands is typically three to five, which is also the most common range for chloride in general [70]. Part of the coordination sphere is made up of water molecules that vary somewhat in exact position. Note that the chloride ion is present under both low and moderately high salt concentrations (Table 5), indicating that it is unlikely to be a crystallization artifact. (PNG 975 kb