Catalytic centres of dimeric cyt bc₁ complex from S. cerevisiae are illustrated in two ways. The structure of the right half shows the inhibitor stigmatellin and the natural substrate UQ-6 in the X-ray structure (pdb 2ibz) as well as their hydrogen bonding partners. His181^RIP1 is also a ligand of the iron-sulfur cluster (FeS). Stigmatellin represents the position of a transition state of ubiquinol (QH₂) oxidation in the Q_o site, and UQ-6 indicates the position of ubiquinone/semiubiquinone (Q/SQ^•) in the Q_i site. The structure of the left schematically shows the Q cycle mechanism. The four highly conserved residues of cyt b (COB): Pro271^COB (P), Glu272^COB (E), Trp273^COB (W) and Tyr274^COB (Y) in the Q_o site form the Q_o motif [14]. Electron transfer in cyt bc₁ complex can also cross the dimeric enzyme (pink arrow) [111]. Owing to the large-scale movement of the extrinsic domain (ED) of Rieske iron-sulfur protein (RIP1), the FeS is shown at two positions, the b-position (based on pdb 2ibz) close to the Q_o site quinol and the c-position close to haem c₁ (based on pdb 1be3). Whereas the Q_o site ubiquinol releases two electrons and two protons upon oxidation, only one electron is transferred to Q_i site, therefore the full reduction in the Q_i site quinone requires oxidation of a second ubiquinol molecule at the Q_o site and the uptake of two protons. The exact sequence of protonation steps at the Q_i site is not differentiated in this simplified scheme. Iron atoms are depicted in brown, sulfur atoms are shown in yellow. The FeS and its ligand His181^RIP1 at the c-position are shown in gray scale. Hydrogen bonds are depicted as dashed lines. Electron transfer pathways are shown in red, and proton release and uptake routes are in green.