Naming of phosphate oxygens

gjacobs at gjacobs at
Sun Nov 26 16:37:29 EST 1995

gabb at (Henry Gabb) writes:
> 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.

Agreed. Even in more regular structures things can get more complex
that a simple case of one of the two pointing towards the major groove.

> : 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.

Basically as I somewhat incorrectly [:-)] suggested.
You have to be a little careful here: what happens at the termini?
In my case, it'd be OK if I used the C5'. That is all the atoms
need to be within the same nucleotide! Pretty obvious really :-)

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