[phenixbb] Attaching H onto phosphate group and ATP

Young-Jin Cho yjcho at brandeis.edu
Tue May 19 08:42:55 PDT 2009

Hello phenix users,

I am wondering if phenix.elbow can attach H onto phosphate group for refinement.  The reason for that, based on different pH environment, phosphate group should have different charges with respect to how many protons attached.
In addition, how can I know normal distance restraints such as ATP? What I only know from the coot is that it shows P-O bond length is 1.61A and P-O bond (delocalized double bond) is 1.5A.  The reason for this is, I heard about phosphate ion, if it is protonated, then the bond length of HO-P is longer than that of non-protonated O-P.  I want to try if is true for ATP as well. Is there anyone who knows practically testing this fact by using phenix?

Thanks in advance,


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