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Several hundred genes in the human and Drosophila (and likely for others
as well) encode zinc finger-containing proteins. Especially well
characterized for transcription factors, for example. The motifs
coordinate with Zn in order to stabilize folding of individual protein
domains.
My first guess would be Zn. And, no surprise that Zn was never
intentionally added and it still crept up in the structure. The source -
from water, your chemicals and you name it.... Guess one needs to watch
out for the EDTA one tosses in during purification - may be more
detrimental than imagined.
Check out this review:
Nyborg JK, Peersen OB.
That zincing feeling: the effects of EDTA on the behaviour of
zinc-binding transcriptional regulators.
Biochem J. 2004 Aug 1;381(Pt 3):e3-4. Review.
Raji
Joel Tyndall wrote:
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Hi Wendy,
I had the same scenario a few years ago. It was zinc (from no obvious
source) and we identified/confirmed it by by X-ray fluorescence at a
synchrotron source
Cheers
J
Wendy Gordon wrote:
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Hello-
Thanks for entertaining my non-ccp4 question...
I am refining a crystal structure at ~2 Angstroms resolution in which I
find a large, unexpected electron density that is potentially a Zinc
ion because it is coordinated by 2 Histidines, 1 Glutamic acid, and
possibly a water molecule.
This site appears as a strong peak in anomalous difference Patterson
maps (the data was collected at SelMet wavelength 0.979 Angstroms and I
believe that Zn's absorption edge occurs around 1.2 Angstroms). The
problem is, I didn't add any zinc in any purification or
crystallization conditions. I DID affinity purify the protein with
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?
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?
Thanks so much!
Wendy Ryan Gordon
