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.
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