Naming of phosphate oxygens

Henry Gabb gabb at
Fri Nov 24 06:24:54 EST 1995

Peter Slickers (slickers at wrote:

: No, OP1 and OP2 will never reverse since P is a prochiral center and since the
: position of P is fixed through O3' and O5'. With OP1 and OP2 it is
: exactly the same kid of problem as with H2'1 and H2'2, but for H2'1/H2'2 
: and H5'1/H5'2 the correct positions are defined by the IUPAC
: recommendation of 1982 (IUPAC. 1983. Europ J Biochem, 131: 9-15.).

I wasn't suggesting "chiral" inversion.  When the phosphate moves, the
phosphate oxygens can both be pointing to the same groove.  Look at a
non-regular nucleic acid like a hairpin loop.  The phosphate position
can hardly be considered fixed relative to the grooves.

: Therefore my question is, if there exist any recommendation for the 
: phoshate oxygens.  

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.

|  Henry Gabb                                 (gabb at   |
|  Imperial Cancer Research Fund                                     |
|  44 Lincoln's Inn Fields                                           |
|  London WC2A 3PX                                                   |
|  United Kingdom                                                    |

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