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,
