Dear all,
I am trying to refine a serine protease crystal structure using REFMAC5.
The density at the protease active site clearly indicates an acyl-enzyme
intermediate as a result of nucleophilic attack on P1 substrate residue by
the active site serine.
The model thus should display serine Og covalently bonded to the carbonyl
C of the C-terminal P1 residue (Ala) while its carbonyl oxygen points
towards the oxyanion hole.
In order to maintain the proper distance and angles for this ester bond
during refinement, how do I define this link between Ser Og and C-terminal
Carbonyl C when using REFMAC?
I would really appreciate your help.
with kind regards,
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