Dilip,
Depending upon your data and the wavelength you collected it at - can you
generate an anomalous difference map? First off - if there is a significant
anomalous peak, this will exclude Magnesium at it's K-edge is at ~9.5Å
You could also compare the peak heights of your unknown metal ions
Hi Dilip,
There are a few things you might try. You have to make sure that all
coordinating atoms (including waters) are in your model. If you refined with
TLS for the protein, try resetting the B-factors for all atoms and refine
without TLS. If this reduces the difference density, you
If the metal center is a stable complex then ICP-OES or XRF (e.g. TXRF)
methods can easily identify and quantify metals present in a small sample
of protein.
Roger Rowlett
Dear All
I have solved a structure of a metal-ion dependent exonuclease enzyme. In
homologous structures, two or three
Dear Dilip,
it's difficult to exactly analyse the coordination of your metal in 2D. But, my
suggestion is :
Try another metal like Zn, which maybe is a contamination (from the plastic of
eppendorf for example). Zn has more electron than Mg maybe that's the reason
why it's still green.
I
Dear Dilip,
I was wondering if the problem was more basic, just about setting the
occupancy in your input pdb file. Try setting the occupancy of Mg to 1 in
your input coordinate file (pdb file) and refine it. If its Mg, it should
turn blue. If its not Mg, the density should turn red instead of
Hi Kumar,
I suggest to try Fe in the active site since it binds with Asp and His which is
typical binding motif of Fe.
Best,
Ping
At 2015-07-09 17:35:10, Dilip Kumar dku...@igib.in wrote:
Dear All
I have solved a structure of a metal-ion dependent exonuclease enzyme. In
homologous
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Hi Dilip,
More information is needed regarding the crystallization condition(s).
Anyway, Mg2+ ions are always (most of the time) are surrounded by water
molecules in their primary hydration sphere...(typical distance should be
2.2 A, if I remember correctly)...and the typical geometry would be
Looks like Ni (II) in the 4-coordination tetrahedral config. Could it be loose
Ni ions from the IMAC column if you’d used one? Ni and Mg have very close
atomic radii and Ni (II) can form the 6-coordinate complex as well.
On Jul 9, 2015, at 4:35 AM, Dilip Kumar dku...@igib.in wrote:
Dear All
Calcium with a His bound, I do not think so.
SVL
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Gyanendra Kumar
[gyanendr...@gmail.com]
Sent: Thursday, July 09, 2015 10:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ambiguous metal ion
Hi,
If you have a crystal you could do a x-ray fluorescence scan to see what
might be in your crystal and collect anomalous data at higher wavelength
close to the manganese edge to see if it is manganese. These enzymes can
also deal with Zinc which is a bit heavier and might be still bound
Dear All,
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