Here's another late addition to the discussion, which Chad's comment
reminded me
of:
We just deposited a similar-sounding structure of a DNA polymerase
(2HVI). The
protein is in the closed conformation, with ddCTP pairing with G in the active
site of the two monomers in the ASU. A third ddCTP binds to the
surface of one
monomer at some distance from the active site.
Josh
Quoting Chad Brautigam <[EMAIL PROTECTED]>:
Hi, Phoebe,
Sorry to jump in late on this one- but I second Stefan's note here.
When soaking dinucleotides (which are poor substrates) into Klenow
Fragment xtals, I noted binding both at the active site and at a
crystal interface site that is likely nonphysiological. The
adventitious site is just big enough to accommodate a dinucleotide-
no binding was observed here with longer oligos. Alas, that
dinucleotide-containing structure is not deposited.
Chad
Stefan Knapp <[EMAIL PROTECTED]> wrote: we see quite
frequently ligands sitting in crystal interfaces in
addition to the described binding site
for example -
STK16, a S/T kinases pdb-code: 2BUJ, the ATP competitive ligand
staurosporine binds to ATP site as well as to a symmetry related
molecule forming a nice aromatic stacking interaction
also quite interesting
CK1 gamma 1 (S/T kinase) pdb-code 2CMW, ATP competitive ligand binds
also to upper kinase lobe
Stefan
____________________
Stefan Knapp
Structural Genomics Consortium
Oxford
UK
22/01/2007 23:29 >>>
A biochemist friend asked for examples of cases were a protein was
co-crystallized with or soaked in a ligand that bound in the wrong
place -
say, because the ligand used wasn't quite the right one or because
other
important ligands were absent.
I'm sure such examples are out there, especially when soaks were done
at
high concentrations, but I'm having trouble thinking of concrete
examples.
Help?
thanks,
Phoebe Rice
---------------------------------------------------------------------------------------------------------------------------
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/index.html
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
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