If you are working on a protein that binds vitamin B12 (cobalamin) then
you may be interested that there appears to be an issue with geometry of
the B12 dictionary currently distributed by ccp4. The problem is that atom
C19 in the corrin ring is defined as being SP2, planar with no hydrogen
atom attached. Small molecule structures of B12 clearly show this atom is
tetrahedral (as do high resolution protein complexes). A survey of 53 PDB
structures containing B12 reveals that 19 have C19 atoms that are not
sufficiently chiral. All are recent - structures prior to 2008 are all OK.
The problem also effects the PDB chemical components definition of B12.
Please see
https://www.globalphasing.com/buster/wiki/index.cgi?B12Dictionary
This page provides a dictionary for B12 with the problem fixed.
Hope this proves useful.
Regards,
Oliver
| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK |
| http://www.globalphasing.com/people/osmart/ |
