Hi All,
I am making a tutorial to illustrate the mechanism of enzyme catalysis of
hydrolysis of an ester. The PDB file that I am using shows the Ser 200 at
the active site covalently bonded to an inhibitor which is bound at the
active site, and does not contain any hydrogen atoms. I added two hydrogen
atoms to the file, one was identified as a Ser 200 atom and the other one as
a His (also at the catalytic site) atom. Both atoms were displayed at
appropriate locations. My problem is that the Ser is no longer bonded to
the inhibitor, even though the Conect commands are still in the PDB file,
and using the Jmol connect command I can show the Ser bonded to the
inhibitor at the appropriate place in the mechanism. I use the connect
command to make, delete or change the nature of other bonds associated with
the active site. I do not understand how the information in a PDB file is
used to make the covalent bonds well enough to know how I affected the Ser
bonding by adding the hydrogens. Any suggestions would be greatly
appreciated.
Karl
Karl M. Oberholser, Ph.D. Phone:
Professor of Chemistry Voice: 717-766-0512
Chemistry & Biochemistry Dept. Fax: 717-691-6046
Messiah College e-mail: [EMAIL PROTECTED]
P.O. Box 3049
One College Avenue
Grantham, Pa 17027
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