We investigate the substitution effects on electron transfer in Rhodobacter (Rb.) sphaeroides reaction center using ab initio calculations. The overlap of molecular orbitals in the X-ray structure of 1PCR of the protein data bank using Gaussian09 can qualitatively explain the tendency of the experimental transition time. The charge effects of proteins on electron transfer in Rb. sphaeroides reaction center are also investigated, by employing a simple point charge approximation for proteins. We have found that the primary effect for the route A orientation is the effect of long side chains. For the route A orientation on the electron transfer, the influence of the charges of proteins operates through the long side chains indirectly as well as directly work to increase the value of overlap integrals.