This is interesting. If the parameters for heme C reflect the molecule before linking to cysteines in the protein, and the modifications will be made as specified by link information in the dictionary, then actually heme C (HEC) should be the same as HEM (heme b, protoheme). HEC is superfluous, unless its definition could include the fact that it must be covalently linked.
Heme C is a regular heme like in myoglobin (heme B, protoheme) that has been attached to a protein via two cysteines. Each Cys Sg adds across the double bond in a vinyl group, the latter consisting of CA connected to ring by single bond, CB connected to CA by double bond. Cys Sg attaches to the CA atom, and the double bond becomes single. However comparing the .cif library files, the double bond in HEC has moved from CA=CB to ringC3=CA: (third letter B or C in the atom names indicates which vinyl group it is in) ccp4-7.0/lib/data/monomers/h/HEM.cif: HEM CAB C3B single 1.474 0.020 HEM CBB CAB double 1.330 0.020 HEM CAC C3C single 1.474 0.020 HEM CBC CAC double 1.329 0.020 ccp4-7.0/lib/data/monomers/h/HEC.cif: HEC CAB C3B double 1.483 0.020 HEC CBB CAB single 1.510 0.020 HEC CAC C3C double 1.483 0.020 HEC CBC CAC single 1.510 0.020 And when I look at a protein containing HEC in coot, it displays a double bond from ring to CA. (By the way in coot "get monomer" HEC comes up with one of the pyrrole rings flipped 90* from the porphyrin plane!) I suggest that either: HEC should be exactly like HEM, and the link definition would include: link SG to CA, add H to CB, and change the double bond to single; Or, HEC should be pre-hydrogenated: vinyl is ethyl, and the link definition just involves removing H from CA and making the link SG-CA. eab If the parameters for heme c reflect themolecule before linking to cysteines in the protein, and the modifications will be made as specified by link information in the dictionary, then actually heme C (HEC) should be the same as heme b (protoheme). On 05/15/2018 04:35 AM, Eugene Osipov wrote:
Dear CCP4 developers, please fix errors with heme c dictionary file HEC.cif. Edward Berry described this problem in detail 4 years ago: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36393.html This error already affects deposited entries, e.g.: 4QO5 clearly contains errors in vynil groups of heme c. -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com <mailto:e.m.osi...@gmail.com>
