Extended Data Figure 5: Electrostatic potential surfaces and computed binding energies.

Charge transfer from the catalytic ensemble (Trp109, Asp113, Trp187 and Asp113-associated water) to the modified nucleosides stabilizes the AlkD–DNA complexes. a, 3d3mA substrate. b, 3mA substrate. c, Transition state (TS) approximation. d, dR⁺ intermediate. Positive charge located on the deoxyribose moiety of the unbound nucleosides relative to that on the unbound dR⁺ intermediate is indicated below the lesions. Charge transferred from the catalytic ensemble to the lesions upon complex formation is indicated above the arrows. Electrostatic potentials were scaled to −0.22–0.55 atomic units on an isodensity surface of 0.05 electrons bohr⁻³. e, Modified nucleosides shown in a–d. f, Computed binding energies (kcal mol⁻¹), differential bond elongation energies (ΔΔE^‡, kcal mol⁻¹), and corresponding rate enhancements (r.e.).