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nickel beads, so potentially it could be a Nickel ion. I should also say that during refinement in refmac where my Zn occupancy is held at 1, that I obtain a negative peak in the 2Fo-Fc in this position, but if I leave the site unoccupied- I get a huge positive peak- so I either have the wrong species defined or my occupancy is not 100%- right?
On the occasions where I've encountered random ions they're usually not 100% occupancy anyway (e.g. chloride at 80%).
Is there any way short of biochemical means (ITC, mutation, etc.) to figure out what species is occupying this electron density? I have thought of atomic absorption- has anyone tried it to determine the metal species in a protein? Does it seem possible that I could have a Zn ion in my protein crystal where the Zn could only come from our standard DI water supply?
Couldn't the Zn come from purification? I'm fairly sure it wouldn't be present in high enough concentrations in the water to result in a large peak in the map. We've used AES to try to figure out why a protein solution was yellow and were told that it bound 2 nickels - which didn't fit anything else we know about the protein, and could easily be left over from Ni purification. But in theory it works.
You could also use a synchrotron for this, but that's overkill unless you have too much synchrotron time. I have a somewhat similar data set but the feature obviously wasn't biologically relevant so I ended up leaving it as a water.
