See below.
Ceeers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 4/17/2014 4:13 PM, Faisal Tarique wrote:
Dear all
Can anybody please explain what is the classical metal ion
coordination for Mg2+, Ca+ and Na+ with Oxygen atom and the average
distance with these metal ions
You can find answers at the MESPEUS database
(http://mespeus.bch.ed.ac.uk/MESPEUS/)
..does the distance vary with the type of metal ion and its
coordination with oxygen atom
Yes. There are "typical" metal-ligand bond distances that are sensitive
to the metal ion, coordination number, and ligand atom.
..what is the best way to identify the correct metal ion in the
electron density in the vicinity of negatively charged molecule mostly
oxygen containing molecule..
A combination of both the bond distances and the coordination geometry
may give you a clue. Bear in mind that X-ray bond-distances in proteins
may not be that accurate--not like small molecule crystallography. But
the distances can still be useful nonetheless.
In one of my paper the reviewer has asked me to check whether the
octahedrally coordinated Mg+ is Ca+ ion..and similarly raised doubt
about the identity of the Na+ ion as well..his argument was based on
metal ion to oxygen distance
This may be challenging, but the MESPEUS database may give you some
clues as to what the typical ranges of bond distances should be. The
best way to prove the existence of a bound metal is to do ICP-OES or
TXRF of your protein sample. Of course, Na, Mg, and Ca are common
contaminants/adventitious metals, so this can be challenging, too.
Especially if you need these in your buffer to populate the protein.
..I am attaching the figure with this mail..i request you to please
shed some light on this area and help me in clearing some doubts
regarding this.
--
Regards
Faisal
School of Life Sciences
JNU
