The two unique sugar binding sites in wheat germ agglutinin, located in the subunit/subunit interface of the dimer molecule and termed primary and secondary binding sites, are compared in the light of the newly obtained chemical amino acid sequence and a high-resolution electron density map (1.8 A). Homology was found in the three amino acid residues directly involved in sugar binding: Tyr73II, Ser62II, Glu115I in the primary site, and Tyr159I, Ser148I, Asp29II in the secondary site (subscripts refer to promoters I and II). Thirteen corresponding side-chain atoms of these three homologous residues in the two sites could be superimposed with a root-mean-square difference of 1.39 A. The three sugar binding residues are located in subsite 1 of each extended binding location and contribute to binding of the terminal, non-reducing N-acetyl-D-glucosamine and N-acetyl-D-neuraminic acid residues only, and they provide three hydrogen bonds for complex stabilization. Two hydrogen bonds are made with the carbonyl and amido portions of the N-acetyl group and the third with the C-3 OH group of the sugar ring. It is suggested that small differences in the sugar binding affinities at these two unique sites exist, due to the different numbers of van der Waals' interactions made at these sites, which contribute to stabilizing, for instance, the wheat germ agglutinin/N,N'-diacetyl-chitobiose complex. The single tryptophan residue is located at a distance of approximately 13 A from the primary site and is thought to have no affect on sugar binding. In addition, the disposition of the four saccharide binding sites of the dimer with respect to three local, pseudo 2-fold symmetry axes, relating domains of opposite protomers, is discussed.