gabb at europa.lif.icnet.uk (Henry Gabb) writes:
> Peter Slickers (slickers at imb-jena.de) 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 :-)
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> | Henry Gabb (gabb at icrf.icnet.uk) |
> | Imperial Cancer Research Fund |
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