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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:[log in to unmask]] On Behalf Of Dhirendra K Simanshu
Sent: Friday, August 26, 2011 10:34 AM
To: [log in to unmask]
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 <[log in to unmask]> 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 <[log in to unmask]> 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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