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 --------------------------------- Be a PS3 game guru. Get your game face on with the latest PS3 news and previews at Yahoo! Games.