Opening Image: Human oxy-Mb. The E and F helices (shown in red) sandwich the heme group (shown in spacefill).

This exercise takes you inside the myoglobin molecule for a closer look at the oxygen-binding site. We begin with the heme, then go on to consider various side chains lining the oxygen-binding pocket.

The view is now restricted to the heme group. Toggle between wireframe and spacefilled models. Heme consists of a porphyrin and an iron atom (orange) in the 2+ oxidation state. The Fe(II) is coordinated to the four nitrogens of the porphyrin ring.

Now use the toggle to return to the wireframe model. Rotate the model so that the plane of the porphyrin is perpendicular to the plane of the screen. Observe that the iron atom is situated 0.55 Å out of the heme plane. If you're having difficulty seeing it, click here to orient.

The iron atom is covalently bonded to the imidazole ring of His F8. This histidine, which occupies the fifth coordination position, is called the proximal histidine. Another histidine residue (His E7), termed the distal histidine, is near the heme on the oxygen-binding side on the heme. However, its imidazole group is too far away from the Fe(II) to coordinate with it. In deoxymyoglobin, the sixth coordination position remains empty; in oxymyoglobin, it is occupied by O₂.

Close-up view of the O₂-heme complex. The α carbons are shown in dark gray. Note the hydrogen bond between the imidazole of the distal histidine and O₂. The model shows the position of His E7 in the crystal. We will return to this point below.

With the exception of the distal histidine, the side chains lining the oxygen-binding pocket are nonpolar.

Let's examine the invariant amino acid residues in the oxygen-binding pocket. Use the toggle buttons to add or remove the amino acid from the visualization. The side chains are shown in green; α carbons are shown in dark grey.

Valine E11 forces the O₂ molecule to tilt away from a preferred perpendicular alignment with the plane of the heme.

Phenylalanine CD1 is invariant in all myoglobins and hemoglobins. Its aromatic ring makes contact with the heme.

Leucine F4 makes contact with both the proximal histidine and the heme.

Now we see a spacefilling model of oxy-myoglobin. But where is the oxygen molecule?

Highlight the side chain of distal histidine. Zoom in.

Toggle wireframe model of the distal histidine side chain.

The distal histidine acts as a "gatekeeper." Its imidazole group is free to swing in and out of the heme pocket. This allows O₂ to enter and leave the pocket. We will continue our discussion of side chains near the oxygen-binding pocket in the next exercise.