Re: [ccp4bb] Unexplained density

[Roger Rowlett]

While it would not be unreasonable for zinc ions to be coordinated to the asp residues (perhaps with bridging waters or hydroxides), I am a little troubled by the lack of electron density around the coordinating residues. If there are zinc ions tightly coordinated at full occupancy, I would normally expect the coordinating residues to be more well-defined, with fairly low b-factors. If you want to play with zincs, I would start by placing two zincs in the blob ends of the density, and constraining the Zn-O links in refmac so the metals don't wander. (The Zn-O bond should be about 2.0 A, and refmac gets this right when you generate the constraints cif file.) Zn(II) typically likes to be four-coordinate, approximately tetrahedral, and usually likes at least one or two softer ligands, like His or Cys. Looks like that can't be the case here--all hard ligands, carboxylates and maybe waters. Cheers. On 4/29/2010 5:38 PM, Daniel Bonsor wrote: Hello again I currently have some unexplained density in my structure. As you can hopefully see from the images (see file), the density is dumbbell shaped. Whatever it is, it is coordinated by Asp and Glu residues. To me it looks like each lobe is a ring structure. The crystallization condition was: 6.5% PEG 8K, 10mM ZnSO4, 100mM sodium cacodylate pH 6.5, 100mM Am2SO4, 1% glycerol, with 20% glycerol as cryo. Protein was originally in 50mM Tris, 50mM NaCl pH 7.5. I originally placed a single Zn at the center of each lobe. Though after refmac, the Zn was displaced to one side. Two zincs in each dumbbell may have worked, but I am dubious about two zinc atoms being 4A apart and there is still some unexplained density. Are there any possible cyclization reactions of Tris, cacodylate or glycerol may have undergone to explain the density? Or is it simply a highly ordered water network? Or is there some other explanation? Thanks in advance Dan -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu