The figures would be more helpful if you told us what each map contour
represented, and at what contour level. I assume blue is 2fo-fc and
green+red is fo-fc, positive and negative. It would be even more helpful
to have the maps to turn over in 3D, but I understand you would probably
be reluctant share that.
The density looks much too strong to be mere water.
Acidic surface residues may bind zinc. The metals might appear at
multiple alternate locations, if the occupancies are less than 1.0.
Synchrotron anomalous maps would be helpful in seeing Zinc, whose K edge
is at 1.28 A.
Multiple alternate locations are likely to show up at special symmetry
positions. I have the impression this may be a special position in your
map, but I can't be certain (2-fold axis?).
Zinc and cacodylate may form cage complexes which can be bound between
multiple surface acid resides (personal observation, not published). The
complexes I have seen have one zinc at each pole with three cacodylates
around the equator. Your density does not look especially similar to the
complexes I have seen.
Cacodylate also has a pretty good peak on anomalous maps, and since it's
peak is at 1.04 A, anomalous maps at multiple wavelengths could
distinguish between arsenic and zinc.
On 04/29/10 17:38, 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
--
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
