Are O carboxy atoms distinguishable in ASP and GLU?

Gerard Kleywegt gkleyweg at laplace.csb.yale.edu
Tue Jun 11 13:31:38 EST 1996


Gerard Pujadas wrote:
> 
>         Hi to all !!
> 
>         My name is Gerard Pujadas and I'm doing studies about protein
> conformation. I would like to know if crystallographs are able to
> distinguish among the oxygen from OH and the oxygen from C=3DO in the -COOH
> group of ASP or GLU side chains. From the IUPAC rules (Biochemistry, 9(18):
> 3471-3479, 1970 it seems that the O atom labelled as 1 (OD1 or OE1) belongs
> to C=3DO and the O atom labelled as 2 (OD2 or OE2) is from O-H (see Table II=
> I
> from page 3477 of the above mentioned paper).

unless you have atomic resolution you can't really be sure
about the protonation state of carboxylates, although
sometimes you can make an educated guess by looking at
salt link/h-bonding partners

if they're indistinguishable, i think the rule is that the
oxygen atom which gives a CHI2/3 torsion in the range -90 to +90
is labelled as "1" and the other as "2"
don't infer anything from these labels concerning the
protonation state though !!!

--gerard2

--------------------------------------------------------
Gerard CD Kleywegt
Presently at Yale (mailto:gkleyweg at laplace.csb.yale.edu)
Normally in Uppsala (mailto:gerard at xray.bmc.uu.se)




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