QM/MM models of the BC3987 active site.

(A) QM/MM geometry optimized structure of BC3987 showing the quantum mechanical and molecular mechanics regions in ball-and-stick and cartoon representation, respectively. (B) Active site (Model I) where the Thr8 residue has the rotamer observed in the crystal structure. The Cys12 side chain is hydrogen bonded to the Cys15 amide proton. The Gln9 amide proton is a possible hydrogen bond donor to the buried Cys15 thiolate. (C) In this structure (Model II) the Thr8 side chain was rotated to resemble the rotamer observed in E. coli and C. ammoniagenes NrdH-redoxins prior to geometry optimization. The Thr8 hydroxyl group and Gln9 amide proton appear to form hydrogen bonds to the buried Cys15 side chain while the Cys12 side chain is hydrogen bonded to the Cys15 amide proton. The link atoms connecting the MM and QM layer in B and C are colored pink.