An ion channel is a selective permeation pathway, not simply an aqueous hole of fixed diameter. A hydrated ion entering a narrow selectivity filter must lose or reorganize some hydration water. The energetic cost can be offset by interactions with charged or polar groups in the pore. Different ionic radii, valences, hydration free energies, and coordination geometries therefore produce different permeation barriers and binding affinities.
A classical potassium selectivity filter presents oxygen ligands that stabilize relatively dehydrated potassium in configurations resembling its aqueous coordination. Smaller sodium does not automatically pass more easily: its hydration is stronger and the filter need not provide a compensating configuration at equally low free energy. Filter flexibility and multi-ion occupancy matter, so the explanation is an energetic balance, not the assertion that a rigid hole simply blocks every larger or smaller sphere. Ion-ion interactions and coupled displacement can permit rapid conduction while maintaining selectivity.[ref]
The structure of the potassium channel: molecular basis of K+ conduction and selectivity by Declan A. Doyle and others. Science 280 (1998), pp. 69–77: structural basis of potassium coordination and selective permeation
Other ion channels use different arrangements. Fixed negative groups can strongly favor divalent calcium over monovalent ions; occupancy and competition then influence both selectivity and throughput. Selectivity is distinct from activation or ion-channel inactivation, which control access or availability. Selective passive flux follows an electrochemical potential gradient; it does not by itself pump ions uphill. Selectivity allows cells to establish particular membrane potentials, generate action potentials, regulate calcium signals, and control solute balance without dissipating every ionic gradient whenever one pathway opens.
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