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. 2013 Aug 27;41(22):10542–10555. doi: 10.1093/nar/gkt756

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© The Author(s) 2013. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 6. — QM/MM simulations. Schematics of the simulated reaction with the chemical step (ET) and proton transfer (PT) events indicated. (A) Potential energy of the hydrolysis reaction by M-PMV dUTPase obtained from QM/MM minimizations along reaction coordinate Q2. The results indicate a synchronous transition state (bond breaking and forming at the phosphorus centre, ET) and a proton transfer step (PT) from W_cat to Asp95 immediately following the chemical step. (B) More O’Ferrall–Jencks plot showing the reaction path in the plane of the bond breaking and bond forming distances obtained by QM/MM minimizations along Q2. The QM region is also shown with the transition state structure.