This animation depicts a novel methodology for visualizing the active of ATP synthase during the synthesis of adenosine triphosphate (ATP). This model is based on the x-ray crystallographic structures of three intermediate states in the reaction coordinate of ATP synthesis. The ribbon (in green) represents the backbone structure of the catalytic β subunit. The site is initially bound by adenosine diphosphate (ADP), inorganic phosphate (Pi), and Mg2+, followed by formation of the transition state and later the formation of the product, ATP. This simulation, in comparison to Model 1, illustrates how the absence of Mg2+ in the substrate-bound state disrupts position and orientation of phosphate within the phosphate binding pocket. The methodology and associated research were published in Biochemistry on February 9, 2012 (see abstract).

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