The quinone 1 processing sites of photosynthetic and respiratory electron transfer chains have spawned an extensive literature dealing with mechanism in the context of structure. This has been dominated by the two-electron gates of bacterial reaction centers (reviewed in Refs. 1 and 2), which until recently have provided the only high resolution structures. Discussion has centered on the features of structure that allow the sites to mediate between the one-electron chemistry of photochemical reactions (or of cytochrome or iron-sulfur center redox reactions) and the two-electron chemistry of quinones. Since reduction or oxidation of the quinone systems involves uptake or release of protons, the sites also have to include the features needed to deal with these processes. Over the last few years, structures at high resolution have become available for several other proteins with quinone processing sites. Among these, the bc 1 complex has provoked the most interest because of the dynamic features associated with the Q o -site, through which ubihydroquinone (quinol, QH 2 ) is oxidized (reviewed in Refs. 3-8). However, recent structures at high resolution have suggested that the second quinone processing site of the bc 1 complex, the Q i -site, through which ubiquinone (quinone, Q) is reduced through a two-electron gate, might also have interesting dynamic features, albeit on a smaller scale (9 -11). Of the three high resolution structures available in which a quinone is modeled at the site, all show marked differences in the pattern of ligation by protein side chains, in the orientation of the quinone, and in the involvement of bridging waters. Earlier studies of functional aspects show the same general two-electron gate behavior at the Q i -site as that at the Q B -site of bacterial reaction centers but with heme b H of the cytochrome (cyt) b subunit acting as an electron donor (12). In both systems, a relatively stable semiquinone (SQ) intermediate stores one electron from the donor chain and is reduced to quinol by a second electron. The involvement of the SQ necessitates that the sites accommodate binding of all three components of the quinone redox system. The three species (Q, SQ, and QH 2 ) require different properties of the H-bond partners, which therefore have to respond during different phases of the catalytic cycle. The structures have shown that the thermodynamic