Oxymyoglobin

Oxymyoglobin is shown with layers of water bound to its surface. 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 Myoglobin page gives more detail on the secondary structure. The а-helices can be shown to form , and myoglobin can be classified as an antiparallel α-helix type of globular protein. 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 a His 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 of the pocket in which the heme is located is colored white, the heme is displayed in spacefill and the atoms located with in 0.5 nm of the heme are displyed as small spheres. Most of these are grey carbons which form the nonpolar environment for the heme. is chelated to Fe²⁺ on one side of the heme.

is chelated to Fe²⁺ on the side of the heme opposite His 93. Fe²⁺ in oxymyoglobin is chelated to six ligands whereas in myoglobin Fe²⁺ has only five of the possible six positions occupied. The binding of O₂ does have an effect on the conformation of the myoglobin. View the , and observe how much Fe²⁺ is off set from being centered in the plane of the heme. Compare this displacement of Fe²⁺ in oxymyoglobin to that in myoglobin by going to Myoglobin, select 'View2:Heme Closeup' from the drop down menu on the right, rotate the image so that you are viewing the edge of the heme. Notice that the Fe²⁺ is displaced to a greater extend in myoglobin than in oxymyoglobin, actually 0.055 nm in myoglobin and 0.026 nm in oxymyoglobin. Check the bottom most box on the right (It may be partially covered) in order to display His 93 which is responsible for pulling the Fe²⁺ out of the plane of the heme. This tug of His is counter balanced with the ₂. is located on the same side of the heme as molecular oxygen and is close enough to the heme to make contact with the O₂ but is not close enough to the Fe²⁺ for its nitrogen to chelate with Fe²⁺.