AMBER Archive (2004)

Subject: Re: AMBER: disulfide bonds

From: Wen Li (
Date: Tue Jan 13 2004 - 12:13:50 CST

Dear Dr. Case,

Thanks you very much for your great help. I was hoping that you could
direct me to some published simulations including zinc finger using
AMBER. Have that been successful?

If the zinc finger motifs are not the major focus in the system that I am
working on, I wonder if it is reasonable that I add some constraints on
these Zn-involved regions in order to avoid to run an MD including Zn.

Thanks again,


On Mon, 12 Jan 2004, David A. Case wrote:

> On Mon, Jan 12, 2004, Wen Li wrote:
> >
> > I am going to perform an MD simulation on a crystal structure which
> > includes several CYS residues in two connected helices. The CYS residues
> > in the two helices are about 3 - 3.5 angstroms away one another in the
> > crystal structure. Should these CYS' be considered to form disulfide
> > bonds? What is the proper distance cutoff for determining disulfide bonds?
> >
> If the two sulfur atoms are less than 2.5 Ang apart, and the coordinates
> are expected to be reasonably good, there is almost certainly a disulfide
> bond. For a distance greater than 3 Ang and (again) good coordinates, the
> bond is probably missing.
> But it is best not to use such rules if you can avoid them, since inaccurate
> coordinates can creep into structures. "Real" PDB files (i.e. from the RCSB)
> will indicate where these bonds are, (and where they are not). Otherwise, you
> have to try to find out how the crystals were prepared, and try to go from
> there. It is likely that the nature of these residues is commented upon in
> the paper describing the crystal structure (if there is such a paper...)
> Also, given the distances you cite, make sure there is not a missing metal
> atom, i.e. that the two cysteine residues are not coordinated to a common
> metal ion. For example, the cysteine sulfurs in a zinc finger structure are
> about 3.8 Ang. apart. (The values you cite are actually quite unusual: too
> long to be a disulfide bond, but really quite short if both cysteines are
> reduced...)
> ...good luck..dac
> --
> ==================================================================
> David A. Case | e-mail:
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA |
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