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 Fe.
The Scale of Things: How large is myoglobin? To find out do the
following:
Select¬Mouse Click Action¬Toggle Distance Monitor
Now use the right mouse button to click on two atoms to find the distance between them. After you are done you probably want to reload the page by clicking in the left frame.
Secondary Structure: Is myoglobin largely helix or sheet? To find out try the following:
Select¬Protein¬Sheet
Select¬Change Color To¬Yellow
Did anything change color? Now try this:
Select¬Protein¬Helix
Select¬Change Color To¬Yellow
Is myoglobin composed of mainly sheet or helix?
Heme Group: Try the following series of commands to display the heme:
Select¬Residue¬HEM
Display¬Ball & 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.
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:
Select¬Protein¬Hydrophobic
Display¬Sticks
Select¬Change Color TO¬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.
Iron Coordination: The Fe atom is coordinated by two Histidine residues, His93 (proximal) and His36 (distal). To view these try the following:
Select¬Residue¬HIS
Display¬Ball & Stick
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:
Select¬Residue¬HOH
Display¬Spacefill¬Van der Waals Radii