[buster-discuss] Zn(?) in special position

[Miguel Ortiz Lombardía]

Hi everyone,

I'm refining a ~3 A structure in a cubic space group where a cysteine
falls near a three-fold axis, so that three cyteines come to be very
close to each other. Close to them and on the three-fold there is a
strong density that I have modelled as a Zn ion giving a reasonably good
agreement with the density. A second peak of density, also on top the
the three-fold completes a nearly tetrahedral arrangement. However, the
distances and angles don't quite correspond to those that I would expect
for such a tetrahedrical arrangement.

If I model these two densities as waters and remove restraints with:

EXCLUDE W|1:O W|1:O
EXCLUDE W|1:O A|59:SG
EXCLUDE W|1:O W|2:O
EXCLUDE W|2:O W|2:O

I get distances of 2.6 A from the water that would be the Zn to each
cysteine and 2.9 A between both waters. In this case there is
considerable positive density in the Fo-Fc map around and between the
two peaks.

If I model the peaks as a Zn and a Cl ions and use:

EXCLUDE B|1:ZN B|1:ZN
EXCLUDE B|1:ZN A|59:SG
EXCLUDE B|1:Z D|2:CL
EXCLUDE D|2:CL D|2:CL

there is no residual density, but the distances make no sense to me: 2.8
for Zn-Cys(SG) and 3.9 for Zn-Cl.

Following some advice in the autoBUSTER wiki I have tried to keep the Zn
tetrahedron with various combinations of distance and angle restraints,
for example:

NOTE B|1:ZN site 3*cys 59 from chain A plus symm and water/Cl
NOTE BUSTER_DISTANCE =2.29 0.05 B|1:ZN A|59:SG
NOTE BUSTER_DISTANCE =2.29 0.05 B|1:ZN A|59:SG SYMM
NOTE BUSTER_UTILANGLE 109.5 4.0 A|59:SG B|1:ZN D|2:CL

but it doesn't work, since both Zn and Cl get out of the axis. If to
these restraints I add:

NOTE BUSTER_DISTANCE +0.001 0.02 B|1:ZN B|1:ZN SYMM
NOTE BUSTER_DISTANCE +0.001 0.02 D|2:CL D|2:CL SYMM

then Zn and Cl stay in the axis but the distances are still wrong (2.6
and 4 A)

Now, it may not be Zn of course and at the moment that is what I
consider most likely. But it looks like it is not water either...

Thank you for any suggestions about what that density could be or any
corrections to the restraints I have tried to use.

Cheers,

-- 
Miguel Ortiz Lombardía

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 86 44
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia