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.png><ATT00001.c><Screen shot 2011-07-07 > at 9.44.55 AM.png>
