This potassium channel (in violet), from the bacterium Streptomyces lividans, was crystallized as a complex with a monoclonal antibody (Fab fragments shown in yellow). That enhances the hydrophilic surfaces, and promotes crystallization, rather than aggregation and precipitation.
This ion channel is composed of 4 identical subunits. Each has two transmembrane alpha-helices, and a third helix that dips into the central channel. A loop from the short helix interacts with 6 of the potassium ions shown. The seventh ion is in the center of the channel.
The 6 ions are bound at the selectivity filter. These ions are stripped of water and are solvated by oxygen atoms from the protein (shown in white). Ions that are too large will not fit, of course, but atoms that are too small (e.g. sodium) will not enter because they cannot be solvated by these fixed oxygen atoms. The seventh is solvated by molecules of water (shown in white).
1k4c (PDB)
Zhou Y, Morais-Cabral JH, Kaufman A, MacKinnon R. Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution. Nature. 2001 Nov 1;414(6859):43-8. (PubMed)
Zhou Y, MacKinnon R. The occupancy of ions in the K+ selectivity filter: charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates. J Mol Biol. 2003 Nov 7;333(5):965-75. (PubMed)
Zhou Y, MacKinnon R. Ion binding affinity in the cavity of the KcsA potassium channel. Biochemistry. 2004 May 4;43(17):4978-82. (PubMed)