The calcium pump goes through a cycle of changes in the process of pumping. Four distinct steps have been proposed, and the PDB currently has structures of two of these steps. The structure on the left, from PDB entry 1iwo
, is the empty state, which presumably has hydrogen ions bound in the transfer site, although they cannot be seen in the crystal structure. It shifts shape into the structure on the right, from PDB entry 1eul
, allowing calcium ions to enter from the top and replace the hydrogen ions, which travel out upwards into the cytoplasm. The remaining two steps use an ATP molecule to shift the shape so that the calcium will be released downwards. In this process, a phosphate is transferred from the ATP to a special aspartate amino acid in the pump, number 351, shown here in red. As you can see, this aspartate and the presumed ATP binding site (which must be close to the aspartate) are some distance from the tunnel that calcium passes through. The switching is controlled by large motions of the ATP-binding domains, which push and pull on the protein surrounding the tunnel, opening and closing it appropriately.