Hello John, We had just such an issue a year or so ago and I posed the same question to the BB. The density that I observed, and the CCP4bb discussion, can be found at:
http://labs.hwi.buffalo.edu/gulick/cyslys.html http://www.mail-archive.com/[email protected]/msg06092.html I was advised to try metals and a variety of oxidation states for the Cysteine. None of which refined satisfactorily. Ultimately, I believe that what we captured was a thiocarbamate or a thiouronium. We modeled the link as such, and have published the density and our best efforts at modeling this in Shah, M. B., Ingram-Smith, C., Cooper, L. L., Qu, J., Meng, Y., Smith, K. S., and Gulick, A. M. (2009) The 2.1A crystal structure of an Acyl-CoA synthetase from Methanosarcina acetivorans reveals an alternate acyl binding pocket for small branched acyl substrates. Proteins 77, 685-698. The Deposited PDB is 3ETC. The paper also describes a few references for chemical precedent. Good luck. Andrew -- Andrew M. Gulick, Ph.D. ----------------------------------- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 ----------------------------------- Hauptman-Woodward Institute Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 7/16/10 4:00 PM, "John R. Horton" <[email protected]> wrote: > Hello! > > I am working on a structure that has continuous density from a Lys Nz atom to > a Cys Sg; these are ~2.9A from each other. I would consider this a H-bond; > however, the 2fo-fc density does not run straight from atom to atom in this > 1.9A structure. At an apx right angle, with the line joining these two atoms > being the hypotenuse, there is aspherical fo-fc density ~2.1A from the Cys Sg > and ~1.7A from the Lys Nz as if another atom sits between these two atoms. > The modeled side chains fit the density very well. No other atoms are close > by to be ligands so I ruled out an ion. > > I'd appreciate any thoughts any of you may have...thanks! > > John Horton > Emory University
