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. Author manuscript; available in PMC: 2013 Apr 10.
Published in final edited form as: J Chem Theory Comput. 2012 Mar 6;8(4):1426–1435. doi: 10.1021/ct200810d

Figure 1.

Figure 1

Key states for the reaction step 1, the nucleophilic attack by Oγ atom of S198 side chain. The geometries were optimized at the QM/MM(B3LYP/6-31G*:AMBER) level. The non-polar hydrogen atoms in oxyanion hole are not shown for clarity. The key distances in the figure are in angstroms. Carbon, oxygen, nitrogen, and hydrogen atoms are colored in green, red, blue, and white, respectively. The backbone of the protein is rendered as a cartoon and colored in orange. The QM atoms are represented as ball and stick, and the surrounding residues rendered as stick. The figures below are represented using the same method.