We have analyzed crystal structures of cytochrome bc1 complexes with electron transfer inhibitors bound to the ubiquinone binding pockets Qi and/or Qo in the cytochrome b subunit. The presence or absence of the Qi inhibitor antimycin A did not affect the binding of the Qo inhibitors. Different subtypes of Qo inhibitors had dramatically different effects on the mobility of the extramembrane domain of the iron-sulfur protein (ISP): Binding of 5-undecyl-6-hydroxy-4, 7-dioxobenzothiazol and stigmatellin (subtype Qo-II and Qo-III, respectively) led to a fixation of the ISP domain on the surface of cytochrome b, whereas binding of myxothiazol and methoxyacrylate-stilbene (subtype Qo-I) favored release of this domain. The native structure has an empty Qo pocket and is intermediate between these extremes. On the basis of these observations we propose a model of quinone oxidation in the bc1 complex, which incorporates fixed and loose states of the ISP as features important for electron transfer and, possibly, also proton transport.