phosphate in protein structure

Pirkko Heikinheimo BTK pheikinh at
Thu Nov 30 00:02:50 EST 1995

Dear X-plor users,

I am refining a protein structure with a phosphate molecule in its active
site. I am sure someone has done a similar refinement before, so to do it
as good as possible I would like to ask a few things:

I have set the O-P-Oangles to 109.5 and the bond length P-O to 1.52 A. Are these
about the right values?

How should I treat the charges? I have now devided the charge -3 between
the four oxygens and set the charge for P to zero. During the refinement
however, I have set off  the charges, as is done for charged residues. Is
this OK? Or should I set one oxygen neutral and devide the charge between
the rest of the phosphate. How should I value the charges then?

I am not building any hydrogens to the phosphate either. I think it would
be hard to know how many to put in, because the exact environment in the
protein active site is hard to estimate. How could I also distinguish the
oxygens from each other (currently at 2.5 resolution)? If I later on would
want to build in hydrogens also, how should I do it?

Thank You for your help!

Pirkko Heikinheimo
Turku Centre for Biotechnology
PO. Box 123,
20521 Turku, Finland

email: Pirkko.Heikinheimo at

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