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Though FAD reduction requires two electrons and protons, only one electron and one proton are accepted by FAD. Acyl-CoA loses two protons and electrons. This is a two step reaction. The first hydrogen being removed by the active center base Glu376-COO- (Acyl-CoA dehydrogenase) as a H+. The second proton is then transferred as a hydride (H-) to the flavin N(5) position. Now, Acyl-Coa becomes unsaturated. FAD gets its seconf proton from the active center of Acyl-CoA dehydrogenase and becomes reduced to FADH2.
But are the two electrons and protons needed for reduction of FAD provided by Acyl CoA ? Where does the 2nd electron come from as Acyl CoA can only looses a H- and a H+ to become unsaturated, Trans-delta2-enoyl CoA.