While I believe there is plenty written about metal coordination, the best
approach, IMHO, is to search PDB for metal of your choice at resolution as high
as you can get and compare to your case.
Vaheh
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Dhirendra
K Simanshu
Sent: Friday, August 26, 2011 10:34 AM
To: [email protected]
Subject: Re: [ccp4bb] Cadmium sites and co-ordinations in structure
Hello Sandeep,
I have been in this situation many times before but with different metal ions..
I have found papers published by Marjorie M Harding very useful in such
situations. In fact, there are lots of information on-line on which is
available here (including all the references for his papers):
METAL COORDINATION SITES IN PROTEINS
http://tanna.bch.ed.ac.uk/
http://tanna.bch.ed.ac.uk/qg3.htm
http://tanna.bch.ed.ac.uk/newtargs_06.html
You will at least find information for Ca and Co here for sure.
All the best
Simanshu
On Fri, Aug 26, 2011 at 10:21 AM, Partha Chakrabarti
<[email protected]<mailto:[email protected]>> wrote:
Hi Sandeep, if someone sends one, kindly share the references.
In general, Ca2+ could have more Asp, Asn kind of coordination and distorted
pentagonal bipyramidal geometry with waters (about 2.5A), Cd can also have S-
since it is softer, I guess Co might have N/O/S (i.e all three with paired
electrons). An inorganic chemistry textbook like Greenwood & Earnshaw or Cotton
& Wilkinson could be handy.. or a bioinorganic chemistry book.
HTH,
Partha
On Fri, Aug 26, 2011 at 7:24 PM, Sandeep
<[email protected]<mailto:[email protected]>> wrote:
Hi,
I crystallised a protein in the presence of Calcium, Cobalt, and Cadmium and
determined its structure. It turns out that I see several metal sites in the
structure, mostly cadmiums. Is there any information published (preferably a
review) which summarises data on cadmium sites in proteins such as for example
the possible coordination numbers of cadmium, distances, type of side chains
found to coordinate with cadmium, etc.? I could extract all this from the PDB,
but a nice review would be simpler to start with.
Thank you in advance for your help
Sandeep
--
Dhirendra K Simanshu
Memorial Sloan-Kettering Cancer Center
Structural Biology Program
New York, NY, USA 10065
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