The electronic asymmetry of the special pair cation radical in the photosynthetic reaction center was studied, using density functional calculations with a polarizable continuum model and a point charge model as the protein environment. The calculated spin density distribution between the halves of the special pair from Rhodobacter sphaeroides agreed well with the experimental value due to the protein polarity effect. The differences in the specific orientations of the ester carbonyl groups of the phytyl groups, as well as the methyl ester groups, are one of the origins of the electronic asymmetry. The orientations of these groups are specific, as revealed by the 14 recent X-ray structures of a variety of type-II reaction centers, with a few exceptions. In addition to the spin density distributions of the special pair cation radical from other species, the structural features of the protein surrounding these groups of a variety of type-II reaction centers were investigated to elucidate the generality and mechanisms of the specific orientations of the groups by a structural alignment and a multiple sequence alignment. The determining factors of the electronic asymmetry among type-II reaction centers are discussed.