I agree with Robbie. It is difficult for an ion to interact with both oxygen (ionised) and amide N-H at the same time. You can also have bifurcated h-bonds
Hope this helps J From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Uma Ratu Sent: Sunday, 24 November 2013 1:15 p.m. To: [email protected] Subject: [ccp4bb] Water or ion Dear All: I use Coot to check water molecules in my model. Most of them are in good coordinates for water. Some of these waters have unusual coordinates. For example, one is in the H-bond distance with 2 nitrogen and 2 oxygen of protein residues, plus one oxygen from ligand (W_230.jpg), and the other is in the H-bond distance with 3 nitrogen, 1 oxygen of protein residue, plus one water(W_300.jpg). Would you advice if these molecules are water, or something else, ions? I tried Coot - "highly coordinated water", and "check/delete water". The program does not pick up anything unusual. Thank you Uma
