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 <[log in to unmask]>:
> 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 <[log in to unmask]> 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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