Homology modeling of the alpha-subunit of Na+K+-ATPase, a representative member of P-type ion transporting ATPases, was carried out to identify the cation (three Na+ and two K+) binding sites in the transmembrane region, based on the two atomic models of Ca2+-ATPase (Ca2+-bound form for Na+, unbound form for K+). A search for potential cation binding sites throughout the atomic models involved calculation of the valence expected from the disposition of oxygen atoms in the model, including water molecules. This search identified three positions for Na+ and two for K+ at which high affinity for the respective cation is expected. In the models presented, Na+- and K+-binding sites are formed at different levels with respect to the membrane, by rearrangements of the transmembrane helices. These rearrangements ensure that release of one type of cation coordinates with the binding of the other. Cations of different radii are accommodated by the use of amino acid residues located on different faces of the helices. Our models readily explain many mutational and biochemical results, including different binding stoichiometry and affinities for Na+ and K+.
Ogawa et al. (2002) studied this question.