The potassium channel is highly selective for K+ over other monovalent cations, and the narrow pore structure with 3 Å in diameter named the selectivity filter (SF) is responsible for the selective permeation. Here we applied the statistical mechanics of liquids called three-dimensional reference interaction site model (3D-RISM) theory, and the binding configurations of the monovalent cations, Li+, Na+ and K+, with special attention on the contribution of water in the KcsA potassium channel were examined. All the three types of cations are bound in the open SF with high affinity, but with different binding coordinations: the in-cage configuration by eight carbonyl oxygens for K+, and the in-plane configuration by four carbonyl oxygens for Li+, whereas both configurations are allowed for Na+. In each case, water contributes an integral part of the ion coordination. In the case of Li+, a linear water-Li+-water complex is settled into two adjacent cages with the Li+ centered at the in-plane site. Positions of water around Na+ are more flexible, which may allow a transition between in-plane and in-cage configurations. K+ stably occupied in-cage configuration, and water occupies adjacent cages. The results provide the distinct configuration of ion and water in the SF, and serves clues for elementary process of selectivity.
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