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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