Dear Oliver,
The representation of B12 has been updated in the wwPDB's Chemical
Component Dictionary and related PDB entries. They will be available
with next week's update of the archive.
Sincerely,
Rachel Green
***************************
Rachel Kramer Green, Ph.D.
RCSB PDB
kra...@rcsb.rutgers.edu
****************************
On 10/12/2012 4:31 AM, Oliver Smart wrote:
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/ |
