The molecule called heme consists of a complex of protoporphyrin IX with Fe(II). Heme is the part of the hemoglobin and myoblobin molecules that binds to oxygen.

Iron-containing proteins can hold Fe(II) in a number of possible ways. Throughout the myoglobin-hemoglobin family, the iron is chelated by a tetrapyrrole ring system called protoporphyrin IX, one of a large class of porphyrin compounds. The basic ring structure of a porphyrin is shown in Figure 7.4a, and protoporphyrin IX is shown in Figure 7.4b. Porphoryrins are also components of chlorophyll, the cytochrome proteins, and some natural pigments. Like most compounds with large conjugated ring systems, the porphyrins are strongly colored. The iron-porphyrin in hemoglobin accounts for the red color of blood, and the magnesium-porphyrin in chlorophyll is responsible for the green of plants.

Heme is noncovalently bonded in a hydrophobic crevice in the myoglobin or hemoglobin molecule (see Figure 7.3). The binding of oxygen to heme is illustrated in Figure 7.5, which shows the oxygenated form of myoglobin. Ferrous iron is normally octahedrally coordinated, which means it should have six ligands, or binding groups, attached to it. As shown in Figure 7.5a, the nitrogen atoms of the porphyrin ring account for only four of these ligands. Two remaining coordination sites are available, and they lie along an axis perpendicular to the plane of the ring. In both the deoxygenated and the oxygenated forms of myoglobin, one of these sites is occupied by the nitrogen of histidine residue number 93.