Re: [ccp4bb] Unexplained density near cobalt
Are the imidazole rings of the histidines distorted? If they are, it could be water/hydroxide. If not, it is probably a cobalt ion side show. Cheers, Rob Meijers EMBL Hamburg --- On Thu, 7/7/11, Artem Evdokimov artem.evdoki...@gmail.com wrote: From: Artem Evdokimov artem.evdoki...@gmail.com Subject: Re: [ccp4bb] Unexplained density near cobalt To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, July 7, 2011, 9:39 PM Could be a hexacoordinated cobalt with a water molecule (or a hydroxyl ion) depending on the chemical environment... Artem On Thu, Jul 7, 2011 at 10:07 AM, Machius, Mischa Christian mach...@med.unc.edu wrote: Y'all, I was wondering if anyone had any thoughts about a feature we observe with a metal-binding site: we have a cobalt that is bound by four histidines and one carboxyl group. There is extra density near the cobalt. See pictures below. The extra density spans the NE2 atoms from two histidines. The Fo-Fc peak (green) has a height of up to 10 sigma (eight molecules in the asymmetric unit, all showing the same feature). I placed a water molecule into the density to get some distances: the distances between the peak and the neighboring histidine NE2 atoms is ~1.8Å and ~2.0Å, resp. The distance between the peak and the cobalt is ~1.7Å. The resolution is 1.24Å. Any input would be greatly appreciated. Many thanks in advance! Cheers! MM
Re: [ccp4bb] Unexplained density near cobalt
Hi MM, Co in its +2 oxidation state typically forms a tetrahedrally coordinated species in high pH environment; and pentagonally coordinated species with five ligands at low pH. A Co ion in its +3 oxidation state forms a octahedrally coordinated species with six ligands. Co +3 is unusual in biological molecules. However it is seen in crystal structures, sometimes with partial occupancy and is a likely product of radiation damage caused by the X-ray beam. In the past I have found that Co+2 is prone to oxidation in the beam if the crystallizing condition has a pH lower than 6.5. Here is a article you might enjoy. Comparison of solution and crystal properties of Co(II)-substituted human carbonic anhydrase II. Avvaru BS, Arenas DJ, Tu C, Tanner DB, McKenna R, Silverman DN. Cheers Balu
Re: [ccp4bb] Unexplained density near cobalt
hey Mischa I would guess that is a split cobalt/metal site occupancy 0.1 and 0.9 or something like that. If you calculate an anomalous difference map you may be able to confirm/reject that suggestion, depending on the strength of the anomalous signal. cheers Preben On 07.07.2011, at 17:07, Machius, Mischa Christian wrote: Y'all, I was wondering if anyone had any thoughts about a feature we observe with a metal-binding site: we have a cobalt that is bound by four histidines and one carboxyl group. There is extra density near the cobalt. See pictures below. The extra density spans the NE2 atoms from two histidines. The Fo-Fc peak (green) has a height of up to 10 sigma (eight molecules in the asymmetric unit, all showing the same feature). I placed a water molecule into the density to get some distances: the distances between the peak and the neighboring histidine NE2 atoms is ~1.8Å and ~2.0Å, resp. The distance between the peak and the cobalt is ~1.7Å. The resolution is 1.24Å. Any input would be greatly appreciated. Many thanks in advance! Cheers! MM Screen shot 2011-07-07 at 9.44.43 AM.pngATT1.cScreen shot 2011-07-07 at 9.44.55 AM.png J. Preben Morth, Ph.D Group Leader Membrane Transport Group Nordic EMBL Partnership Centre for Molecular Medicine Norway (NCMM) University of Oslo P.O.Box 1137 Blindern 0318 Oslo, Norway Email: j.p.mo...@ncmm.uio.no Tel: +47 2284 0794 http://www.jpmorth.dk
Re: [ccp4bb] Unexplained density near cobalt
We have a manganese binding protein that binds two Mn ions in a binuclear complex. It turns out that one of the metal ions can move about 2.0 Å depending on crystallization data collection conditions (check out PDB files 1ON1 and 2F5D for the alternate conformations). In some instances we could see both positions occupied within the same crystal (it looked a lot like what you are seeing under those circumstances). Peaks in the anomalous difference Fourier maps were the clearest evidence that it was manganese in each of the positions. Good luck, Arthur Arthur Glasfeld Department of Chemistry Reed College 3203 SE Woodstock Blvd. Portland, OR 97202 USA On Jul 7, 2011, at 8:07 AM, Machius, Mischa Christian wrote: Y'all, I was wondering if anyone had any thoughts about a feature we observe with a metal-binding site: we have a cobalt that is bound by four histidines and one carboxyl group. There is extra density near the cobalt. See pictures below. The extra density spans the NE2 atoms from two histidines. The Fo-Fc peak (green) has a height of up to 10 sigma (eight molecules in the asymmetric unit, all showing the same feature). I placed a water molecule into the density to get some distances: the distances between the peak and the neighboring histidine NE2 atoms is ~1.8Å and ~2.0Å, resp. The distance between the peak and the cobalt is ~1.7Å. The resolution is 1.24Å. Any input would be greatly appreciated. Many thanks in advance! Cheers! MM Screen shot 2011-07-07 at 9.44.43 AM.pngATT1.cScreen shot 2011-07-07 at 9.44.55 AM.png
Re: [ccp4bb] Unexplained density near cobalt
Could be a hexacoordinated cobalt with a water molecule (or a hydroxyl ion) depending on the chemical environment... Artem On Thu, Jul 7, 2011 at 10:07 AM, Machius, Mischa Christian mach...@med.unc.edu wrote: Y'all, I was wondering if anyone had any thoughts about a feature we observe with a metal-binding site: we have a cobalt that is bound by four histidines and one carboxyl group. There is extra density near the cobalt. See pictures below. The extra density spans the NE2 atoms from two histidines. The Fo-Fc peak (green) has a height of up to 10 sigma (eight molecules in the asymmetric unit, all showing the same feature). I placed a water molecule into the density to get some distances: the distances between the peak and the neighboring histidine NE2 atoms is ~1.8Å and ~2.0Å, resp. The distance between the peak and the cobalt is ~1.7Å. The resolution is 1.24Å. Any input would be greatly appreciated. Many thanks in advance! Cheers! MM
