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In a biological reaction involving an enzyme, the inactive site of the substrate does not directly participate in the reaction.
Most biological reactions involving an enzyme operate through the Induced fit mechanism. In this kind of mechanism, the active sites of the substrate bind to the active sites of the enzyme by a geometrical conformational adjustment, forming an intermediate complex which lowers the activation energy for the reaction and speeds up the reaction rate.
Only the active sites of the substrate and the enzyme are directly involved in the reaction, so the Inactive sites of the substrate will not participate in the reaction.
