Naming of phosphate oxygens

Peter Slickers slickers at
Mon Nov 27 13:13:36 EST 1995

Henry Gabb wrote:

> The only method that I can think of to distinguish the phosphate oxygens
> and the C5' hydrogens is to look down the rotatable bonds in the backbone
> (in either the 5' to 3' or 3' to 5' direction) in assign a handedness to
> them.  It isn't too mathematically difficult and it would solve the atom
> identification problem that you're having in your rms calculations.

Mathematically it is no problem to distinguish between O1P and O2P and 
I already have a program to do that. The remaining question is just 
how to name the results. I have realized now that there is no rule which would
allow to say that the naming in a certain pdb file is wrong or right. 

So I decided to take the Drew-Dickerson dodecamer '1BNA' which was the
first DNA crystal structure with atomic resolution as standard, but later 
on I recognized that in the newer Dickerson structures like '3DNB' and 
in pdb files of modelling programs the naming of O1P and O2P is done 
just in the other way. Now I am trying to apply the pro-S/pro-R 
nomenclature to the phosphate group in the nucleic acid backbone. 
Maybe a chemist can tell me wether O1P in pdb file '1BNA' is 
in the pro-S or in the pro-R position.  


Peter Slickers                                  slickers at
Institut fuer Molekulare Biotechnologie
Beutenbergstrasse 11, Jena                      Tel.: +49-3641-65-6202
Postfach 10 08 13, D-07708 Jena, Germany        Fax:  +49-3641-65-6210

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