Naming of phosphate oxygens in nucleotides

gjacobs at gjacobs at
Thu Nov 23 17:01:13 EST 1995

(Peter Slickers) writes:
> Deoxy-nucleotides have three prochiral centers -- C2', C5', and P. 
> This prochiral centers are carrying two identical substituents but
> although it is possible to assign unambigously a unique name to 
> each substituent. This is done in IUPAC recommendations of 1982 
> (1983. Europ J Biochem, 131: 9-15.) for H2'1, H2'2 of C2' and 
> H5'1, H5'2 of C5'.  H2'1 and H5'1 are pro-S whereas H2'2 and H5'2 are 
> pro-R. 
> DOES anybody knows if there is any recommendation for the naming of the 
> two phosphate oxygens OP1 and OP2 according to their position in 
> relation to the central P ?

I was asking PDB about this a few weeks back and the short answer is
that there is no defined rule... sigh. One structure I looked at
had all notated in one orientation, bar one as if a seeming act of
whimsy. The other structure I examined had them all notated the in
opposite orientation.... silly, huh?
You are obviously running into the same thing: atoms in equivalent
orientations should have the same names or it makes dicussing a
comparison of them an exercise in frustration.

> The structural meaning of this would be, whether OP1 is pointing towards
> the minor or the major groove in a DNA double helix. 

I thought this way too, but really chirality ought to be used. (e.g.
look down the O5' - P bond and assign the names in clockwise order
(O1P then O2P) or something like that.

> Peter
> ---
> 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

Grant Jacobs
<ghj at>

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