The oxygen does not bind to any of the atoms in the peptide. Rather,myoglobin binds a prosthetic group called heme and the oxygen binds to the Fe atom within the heme group. The heme group itself is composed of a protoporphyrin ring containing a bound Fe2+ ion.
The Scale of Things: How large is myoglobin? To find out do the
following: Secondary Structure: Is myoglobin largely helix or sheet? To find out try the following: Heme Group: Try the following series of commands to display the heme: Heme Binding Pocket:
To get a sense of the environment around the heme group you can try the following things. First, select hydrophobic amino acids, render them as sticks, and color them yellow:
Iron Coordination: The Fe atom is coordinated by two Histidine residues, His93 (proximal) and His36 (distal). To highlight all of the His residues try the following: Waters: In addition to the protein and the heme, there are also a number of water molecules that are part of the myoglobin structure. These are water molecules that are considered to be part of the structure because these locations are almost always occupied by a water molecule. To display these waters try the following:
Measurement ¬ Click for distance measurement
Now use the right mouse button to click on two atoms to find the distance between them.
Color ¬ Atoms ¬ By scheme ¬ Secondary Structure
Helicies are red, sheets are yellow. Is myoglobin composed of mainly sheet or helix?
Select ¬ Hetero ¬ Ligand (Hetero and not solvent)
Style ¬ Scheme ¬ Ball-and-stick
You should now see the heme group displayed. One edge of the heme group is deeply buried within the protein while the other edge is on the surface. The Fe atom, which is in the center of the heme, is colored yellow. The oxygen molecule is shown as two red spheres next to the Fe atom.
Select ¬ Protein ¬ All
Style ¬Scheme ¬Sticks
Select¬ Protein ¬Nonpolar
Color ¬ Atoms ¬ Yellow
There are a large number of hydrophobic residues that line the binding pocket. Since the heme group is also hydrophobic it binds with high affinity.
Select ¬ Protein ¬ By residue name ¬ His
Color ¬ Atoms ¬ violet
Select ¬ Hetero ¬ All water
Style ¬ Scheme ¬ Spacefill