NH4+ vs H2O

[Pete Dunten]

Thanks for all the replies.

I was directed to a reference:

Axelsen et al. Protein Science Vol. 3 (1994) pp 188-197
   fascinating work in which a ligand is discovered
   in the active site gorge of AChE after checking a
   Fo - Fc map with data from 20 - 2.8 A.  The ligand
   +(CH3)3 N (CH2)10 N (CH3)3+ was originally modelled as
   5 water molecules based on a Fo - Fc map with data
   from 8 - 2.8 A.  In addition, evidence is presented
   that 2 other waters are probably NH4+ ions.

Gerard Kleywegt grepped the pdb for me, finding NH4
in 1pal and 2act, ND4 in 2mb5, and AMMONIUM ION in 3chy.

Raul Cachau pointed out that it's much worse than NH4+ vs. H2O.
   There are also Na+, Mg++, F-, H3O+, etc, etc to
   consider!
                       -Pete