Re: [o-info] Re: [ccp4bb]: Disulfide bridge

[<deh22@cornell.edu>]

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Thanks for all your quick responses!

Here are a few details (these are unrefined measurements):

S-?-S angle = 94.2
S1-? distance = 2.88 A
S2-? distance = 2.74 A

I purified with a cobalt-affinity column.  That is the only time the
protein had contact with a heavy metal (other than sodium...), so I
doubt it is mercury.

The putative metal position has density showing up in an fo-fc map at a
sigma level greater than 11.

The problem with a metal there is that there are no water molecules
around for coordination.  The cysteines are on the surface of the
protein, but there is no fo-fc density for waters.  It is near (~5 A) an
aromatic ring in a bound inhibitor.

Thanks,
Darrell


Jim Nettles wrote:
> 
> Also. What would the S-?-S distances be?
> 
> Jim N.
> 
> Laurence Pearl wrote:
> 
> > You could have a metal bound into the disulphide - this has been done
> > intentionally in the past by reacting disuphide-bonded protein with
> > Hg1+ which opens the disulphide, gets oxidised to Hg2+ and remains
> > bound between the two sulphurs. More prosaically it could be a iron,
> > zinc or even nickel from a metal chelate column. If you put ? into the
> > structure what would the S-?-S angle be ?
> >
> > Laurence Pearl
> >
> > On Wednesday, September 11, 2002, at 03:08 , <deh22@cornell.edu> wrote:
> >
> >> ***  For details on how to be removed from this list visit the  ***
> >> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >>
> >> Dear all,
> >>
> >> Has anyone ever seen a disulfide bridge that looks something like this:
> >>
> >> Cys-S-?-S-Cys
> >>
> >> If I force the disulfide bridge, the geometry does not fit the density
> >> at all.  If I let the sulfurs fit into the density correctly, the
> >> geometry does not work for a disulfide, although there is very clear
> >> density between the sulfurs.
> >>
> >> Any suggestions?
> >>
> >> Thanks,
> >> Darrell Hurt
> >>
> >>
> 
> _________________________________________
> Jim Nettles
> Chemistry/Pharmacology
> Cherry L. Emerson Center E469
> Emory University Atlanta, Georgia 30322
> (404)377-1475 jnettle@emory.edu