I'm not quite sure why you're studying very specific ion gated channels when you havn't quite got a grip on proteins yet. I'm not trying to be condescending, just wondering if you're teaching yourself or if you're enrolled in a course that's throwing this at you without prior knowledge of general protein biology.
Anyhow, remember that the tertiary and quaternary structure of a protein is dictated by the four weak interactions [ionic, Van der Waals, hydrogen bonds, hydrophobic interactions]. A ligand binds to the protein by weak interactions as well. Most proteins are very specific for their ligands. In other words, the shape of the protein in it's unbound state naturally allows for close contact with the ligand. When a ligand forms bonds with the protein, other bonds are disrupted all along the structure of the protein. This causes a rearrangement in shape.
You've misunderstood me somewhere along the line. The protein is a transmembrane protein. In other words, one end is on the inside of the cell, and the other end is on the outside. Think of it as a tunnel. When the protein is in it's natural conformation, the tunnel is closed (because of the shape). When the ligand binds, the channel opens up. In this case, ions flow through when the channel is open.