NOTES:
In
the first step of the chymotrypsin catalytic mechanism, the oxygen of Ser195's
hydroxyl group covalently bonds with the carbon of the Trp252-Thr253 peptide
bond. At the same time, serine's hydroxyl hydrogen migrates to His57. Run
the "First script" to see the residues involved in this reaction.
Halos have been put around the four atoms involved in the reaction, to make
them easier to see. Rotate the system so that His57, Ser195, and the
peptide bond can be seen easily.
Click on individual residues
in the left column to add or remove them from the picture. If
necessary, click on "fit to screen."
When ready, run the "Second
script" to make the geometric change. First, the O-H bond will be
deleted, and the new bonds (C-O and N-H) will be made. A two second
delay allows these changes to be seen, then the geometry will be optimized.
Once it is complete, use the instructions in the second script's file, "Chymotrypsin_Make_Step_2_2.txt"
to save the changed geometry. The only change is to Ser195, so this is
the only residue that needs to be saved. |