Friends,
With reference to the original post asking about methods to distinguish water
molecules from Sodium and Potassium ions in electron density maps and the and
the follow-up posting which suggested that sinf Na+ and K+ do not form
hydrogen bonds then one can make the necessary distinction based upon the
nature of the side chains near the subject peak. With temerity I suggest
that this is by no means the complete story. Both Sodium ions and H20
molecules have 10 electrons and both will occupy locations about 3 angstroms
from ionised carboxylate groups (these are the only kind which exist on the
periphery of proteins) - hence they are indistinguishable. On the other hand
a water molecule will happily reside 3angstroms away from a neutral aromatic
NH group,or a protonated alkyl primary secondary or tertiary amine (>NH+,
>NH2+, or -NH3+ groups) but a sodium ion will be found elswhere because of
charge repulsion. Hence the simple rule, - and the only one that is valid in
this simple context, "if it's near an amine function it's most likely not a
sodium ion". Rules for K+ ions are the same as for Na+ but here there are an
additional 8 electrons and so peak height will distinguish - if the site is
fully occupied.
Sorry for the lecture in basic chemistry - I had a few moments to spare and
needed the typing practice.
Best wishes =Graheme=
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