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
---
Peter Slickers slickers at imb-jena.de
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
