Naming of phosphate oxygens in nucleotides

gjacobs at gjacobs at
Sun Nov 26 16:31:13 EST 1995

gabb at (Henry Gabb) writes:
> Peter Slickers (slickers at wrote:
> [deleted]
> : 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 ?
> To the best of my knowledge, nobody makes the distinction between these
> substituents because there is rarely a reason to do so.  At least I can't
> think of any right now.  They are chemically equivalent.  Just out of
> curiosity, why do you want to distinguish between them?

Just to given another example: I am looking at protein-DNA complexes.
Imagine I have superimposed two related interactions. Unfortunately,
the OP's have inequivalent names despite being clearly equivalent...
it makes it pretty confusing when it comes to discussing the 

Grant Jacobs
ghj at

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