Plastid terminal oxidase is an integral membrane protein, or more specifically, an integral monotopic protein and is bound to the thylakoid membrane facing the stroma. Based on sequence homology, the enzyme is predicted to contain four alpha helix domains that encapsulate a di-iron center. The two iron atoms are ligated by six essential conserved histidine and glutamate residues – Glu136, Glu175, His171, Glu227, Glu296, and His299. The predicted structure is similar to that of the alternative oxidase, with an additional Exon 8 domain that is required for the plastid oxidase's activity and stability. The enzyme is anchored to the membrane by a short fifth alpha helix that contains a Tyr212 residue hypothesized to be involved in substrate binding.