Fig. 3: Active sites and proton transfer pathways of cyt aa₃ oxidase.

a D- and K-proton channels. Constituents of the channels are shown with side chains for protonable and polar residues and the cryo-EM map (blue mesh) for water molecules (blue spheres). Labels of key residues are boxed and conserved residues are underlined. Residues belong to subunit CtaD if not otherwise labelled. Shown in green (carbon atoms) are the elements of protomer 2 (including azide ion (N₃⁻)). D-channel residues with different side chain conformation in protomer 1 are superimposed (yellow carbon atoms). b Close-up view of structure and cryo-EM map (blue mesh) at catalytic centre highlighting molecular oxygen and the alternate conformation of Glu267. The coordination of Cu_B is shown with dotted lines, the His265 ligand is covalently bound to Tyr269. PLS denotes the proton loading site. Propionate δ and α of haem a₃ are labelled as PRD_a3 and PRA_a3, respectively. c Hydrophobic tunnel with dioxygen molecule bound. The two entries at Ile181 and Leu233 face the intercomplex cavity. The tunnel (beige surface) is calculated for Glu267 in down conformation. d Proton release route. Superimposition of protomers 1 and 2 highlights conformational states of haem a₃ PRD and of conserved protonable residues. Colour codes differentiate carbon atoms, water molecules and Mn²⁺ of the two protomers as indicated. Ex3 denotes the proton exit pathway. The dotted lines indicate H-bonds. Map contour levels were set to 1.0 rmsd. Supplementary Fig. 10 shows the respective cryo-EM map with distances.