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I want to summarize my findings about the heme library and finish this thread: 1)The heme coordinates in HEC.cif contain errors for B ring: it is turned by 90 degrees relatively to heme plane. 2)HEC in PHENIX is not the same as in CCP4. It does not contain coordinates for heme and could not be used for molecule generation in COOT. But it contains correct restrains. Particularly, in PHENIX version of HEC.cif CBB atom excluded from B-ring planarity group, while in CCP4 CBB belongs to plan-7 group. I made HEC.cif for myself from both CCP4 and PHENIX versions of HEC.cif. Maybe someone will find it useful so I attach modified HEC library to this mail 2018-05-16 1:19 GMT+03:00 Edward A. Berry <[log in to unmask]>: > 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:[log in to unmask] >> 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: [log in to unmask] <mailto:[log in to unmask]> >> > -- 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: [log in to unmask]