A key site of ATP synthesis is the mitochondria. Here we see ATP synthase, along with other complexes, embedded in the inner membrane of the mitochondria. Notice the proton gradient formed by the high concentration of hydrogen ions above the inner membrane and the lower concentration below the membrane. ADP and Pi are now visible. These molecules are the substrates for ATP synthesis. A hydrogen ion, or proton, enters the ATP synthase complex. The upper part of the ATP synthase complex rotates as each new proton enters the complex.