Cadmium sites and co-ordinations in structure

From: Sandeep

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

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From: Partha Chakrabart

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

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From: Dhirendra K Simanshu

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

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Dhirendra K Simanshu

Memorial Sloan-Kettering Cancer Center

Structural Biology Program

New York, NY, USA 10065

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From: Oganesyan, Vaheh

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 

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From: Boaz Shaanan

Hi,

I recall seeing some (old) ConA structures with Cadmium substituting for one of the native metals (Ca+2 or Mn+2). They must be in the PDB database.

       Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105

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From: Roger Rowlett

Cadmium(II) prefers softer Lewis bases (e.g. thiolates and imidazole ligands more than carboxylates) and is  commonly found in a four-coordinate environment, similar to zinc(II).

Cheers,

--

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Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

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From: Arthur Glasfeld

While it's not a review on protein binding sites, the following review might be helpful in understanding its chemistry:

Holloway & Melnik (1995) Main Group Met. Chem. 451-585.

Also, David Giedroc has written a couple of useful reviews that include discussions of cadmium binding proteins.

Cadmium is kind of a generalist.  It will bind to sites tailored for calcium, manganese and zinc quite readily, accepting a wide range of protein ligands. Biologically, most cadmium-specific proteins use softer ligands (cysteines) since other metals are relatively less attracted to those sites.   You may see some coordination positions taken up by chloride if you have a high enough concentration in your buffer.

Good luck,

Arthur