The herbicide binding site of the D1 protein in Photosystem II from spinach was modeled on the basis of the homologous L subunit of the photosynthetic reaction center of the bacterium Rhodopseudomonas viridis (Deisenhofer, J., Epp, O., Miki, K., Huber, R. and Michel, H. (1985) Nature 318, 618–624), and on the assignment of functional amino acid residues occurring in these two protein subunits. The overall structure of the L subunit with α-helices D, DE and E was assumed to be conserved in the D1 protein, although the loops connecting helices DE, E and D, DE were enlarged by 3 and 14 amino acid residues, respectively. Protein data bank searches for appropriate loop structures were performed, but none was found to be compatible with experimental data. The binding positions of some herbicides and of the natural substrate in the spinach Photosystem II are proposed and discussed in terms of different binding modes, and interpreted on the basis of data obtained from mutant D1 proteins.