This iron-containing enzyme has two units, each containing haem systems situated in pairs.

Each unit has one haem system (C-haem, electron acceptor) which is covalently bound and used for electron transfer.
The axial coordination sites of the iron atom are occupied by one histidine and one methionine.

The second, not covalently bound system (d₁-haem) is the active site for degradation of the substrate molecule (NO₂^-). One axial position of the iron atom is occupied by a histidine and the second one is the place of the nitrite reduction. The finally formed NO (in this particular bacterial nitrite reductase) is replaced by a hydroxo ligand. The resulting situation is shown in the protein structure shown below.