Properties of proteins

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.