Properties of proteins: Difference between revisions
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== Ideal metal bond distances == | == Ideal metal bond distances == | ||
* classic paper: Harding, M. (1999) [http://journals.iucr.org/d/issues/1999/08/00/ad0073/index.html The geometry of metal-ligand interactions relevant to proteins] | * classic paper: Harding, M. (1999) [http://journals.iucr.org/d/issues/1999/08/00/ad0073/index.html The geometry of metal-ligand interactions relevant to proteins] | ||
* webservice (2006) http://tanna.bch.ed.ac.uk/index.html | * webservice (2006) http://tanna.bch.ed.ac.uk/index.html | ||
* database (2008) http://eduliss.bch.ed.ac.uk/MESPEUS/ | * database (2008) http://eduliss.bch.ed.ac.uk/MESPEUS/ | ||
== Distinguishing ions from waters == | |||
A paper exists about the bond valence method (Acta Cryst. | |||
2003 D59 32-37). Subsequent experience has shown that although | |||
this method works well for identifying ions such as Mg2+ and Ca2+ with | |||
good resolution data, it is not reliable in other cases such as Na+. | |||
Whereas Cl- can often be seen in anom maps, Na+ has a lower f". | |||
There are however some tentative indicators for Na+. The bond valence | |||
sum (the sum of the 'bond orders' to the surrounding atoms estimated | |||
from the distances) tends to be higher than for Cl- or H2O. | |||
Tetrahedral coordination is more likely to be water or Cl-, Na+ | |||
prefers 5 or 6 neighbors. And of course two cations (or two anions) | |||
that are close to each other should not have an occupancy sum greater | |||
than unity. | |||
Revision as of 10:00, 17 February 2010
Ideal metal bond distances
- classic paper: Harding, M. (1999) The geometry of metal-ligand interactions relevant to proteins
- webservice (2006) http://tanna.bch.ed.ac.uk/index.html
- database (2008) http://eduliss.bch.ed.ac.uk/MESPEUS/
Distinguishing ions from waters
A paper exists about the bond valence method (Acta Cryst. 2003 D59 32-37). Subsequent experience has shown that although this method works well for identifying ions such as Mg2+ and Ca2+ with good resolution data, it is not reliable in other cases such as Na+.
Whereas Cl- can often be seen in anom maps, Na+ has a lower f".
There are however some tentative indicators for Na+. The bond valence sum (the sum of the 'bond orders' to the surrounding atoms estimated from the distances) tends to be higher than for Cl- or H2O. Tetrahedral coordination is more likely to be water or Cl-, Na+ prefers 5 or 6 neighbors. And of course two cations (or two anions) that are close to each other should not have an occupancy sum greater than unity.