Molecular Structure Properties of Heme Group in the Oxymyoglobin Protein (1mbo.pdb) Using PyMOL & UCSF Chimera

Abstract

PyMOL and UCSF Chimera are open source multifunctional molecular visualization system developed for the use in structural biology. Both of these tools are well designed with various visualization options available for the user; with the help of such options, we have observed that the iron core binds oxygen in the heme group of oxymyoglobin. Also, various molecular surfaces, internal structures as well as bond lengths between the iron core & molecular oxygen in the heme group and that to the histidine-93 of the oxymyoglobin protein have been calculated. Implementing structural analysis feature of UCSF Chimera, the distance between iron core of heme group and molecular oxygen and that between iron core and histidine 93(H93) have been estimated and found to be 1.827 Å and 2.065 Å respectively which are in good agreement (within 0.5% error) with the bond lengths calculated by x-ray diffraction method ^[4] .The small value of bond length between Fe and O₂ suggests the higher stability of oxygen which is important for transportation, activation and storage of enzymes to support life of living organisms on the Earth. So, it provides an insight in enzymology like oxygenase. Interestingly, oxymyoglobin protein or its constituent amino acid chain may have important role in the origin of early life on the Earth.