Diagram generated with DISPLAY, P. Sherwood, CLRC Daresbury Laboratory
Four possible orientations for the active site water were considered.
Models were constructed using the side chains of Asp-32, Asp-215, Gly-34, Gly-215, Ser-35 and Thr-218
The most stable configuration was determined by optimising each geometry at the SCF level (4-31G basis set)
MP2 calculations predict that structure Ia is the most stable. However, in this orientation the lone pairs on the water oxygen point away from the active site binding cleft and therefore the water molecule is in a catalytically inert orientation. Further modelling has shown that substrate binding forces the water molecule to adopt a more favourable orientation prior to nucleophilic attack.