Oxymyoglobin

Oxymyoglobin is shown with layers of water bound to its surface^[1] This water is strongly attracted to the protein and is part of the structure of any crystalline protein. Hiding the reveals that the overall tertiary shape is much like a hockey puck. The is a prominent secondary structural component. The α-helices can be shown to form , and myoglobin can be classified as an antiparallel α-helix type of globular protein. The Myoglobin page gives more detail on the secondary structure. The shows most of the residues involved in an α-helix are clustered in the area of the plot where one would expect them to be. (Review Ramachandran Plot.) Many of the residues that are outside of the expected cluster are at the end of a helix, and it is not unusual for such residues to have ψ and φ values that are outside of the range for the α-helix. Also notice that many of the residues that are in the quadrants on the right are Gly. (Residues can be identified by hovering over the sphere with the cursor.) The prosthetic group of myoglobin is a , and as shown here it is inserted into a pocket which is nonpolar. Empty heme pocket lined with shows that except for some oxygen on the bottom and His 93 at the mid point of one side the pocket is lined with nonpolar carbon atoms. The mostly inserts into this pocket with the two carboxylate groups of the heme being on the molecular surface. Detailed description of heme structure. The shown in the pocket with the pocket's surface colored white so that the heme can be distinguished from the protein surface atoms. is the fifth ligand chelated to Fe²⁺ (the other four are the nitrogens in the pyrole rings), and it binds to one side of the heme. Show displayed as spacefill that are within 0.5 nm of the heme. These are the atoms which form the surface of the heme pocket and serve as a reminder that except for the ones on the surface of the molecule most of these atoms are carbon atoms and produce a nonpolar environment for the heme. This nonpolar, water-excluding environment is important for the function of myoglobin. Whenever Fe²⁺ is in an aqueous environment and it contacts O₂, Fe²⁺ is oxidized to Fe³⁺. Myoglobin with a heme containing Fe³⁺ (called metmyoglobin) can not fulfill its physiological function and therefore must be degraded.

is located on the same side of the heme as molecular oxygen but is not close enough to the Fe²⁺ for its nitrogen to chelate with Fe²⁺, but it is close enough to the heme to hydrogen bond with the O₂, remember that hydrogens are not displayed in this model.

Other Ligands Binding at the Sixth position

• ; through the carbon, and interferes with its binding. The free heme binding constant is 25,000 times greater for CO than for O₂, but when binding to myoglobin the difference is only 250 times. This lower affinity for myoglobin prevents the very small amount of metabolically formed carbon monoxide from binding to myoglobin, but the amount that may be present in the atmosphere can be large enough to result in binding to myoglobin and causing death of the individual.
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