Hi, I am modellig a structure of an hemoglobin with the four heme groups bonded to oxygen.
To do the alignment I refer to heme as "h" and oxygen as "o".
The template model is the oxy hemoglobin at 1.25 Angstrons resolution Pdb id: 2DN1.
The final model has heme and oxygen, but the iron configuration is OUT of the plane of porphyrin ring toward proxymal His which is bonded to iron.
This configuration is different as observed in oxygen ligated form of hemoglobin in which the iron is in the SAME plane of the porphyrin ring.
In summary, the final model has an heme group in a configuration observed in deoxy form (iron out of the porphyrin plane). I wish it looks like appears in oxy form (iron inside the porphyrin plane).
I appreciate any kind of suggestions.
Flavio