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. 2007 Nov 2;94(4):1412–1427. doi: 10.1529/biophysj.107.111096

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Ternary DlADH·NAD⁺·PYR complex with the ionization scenario of the catalytic triad after 5 ns of MD. (A) Amino acids lining the R1 (wire model in green) and R2 (wire model in blue) subpockets of the active site. The nicotinamide and ribose ring of NAD⁺, the catalytic triad (Ser-138, Tyr-151, and Lys-155), and PYR are shown as stick models with coloring according to the atom type (carbon-yellow, nitrogen-blue, oxygen-red, and hydrogen-gray). The ribbon represents the C-terminal loop of the other subunit acting as a lid of the active site cavity. PYR is shown both before and after the 5 ns of MD. The ring was parallel to the nicontinamide ring of the NAD⁺ ring at the start of the MD but tilted to perpendicular during the MD. (B) Fluctuation of atomic distances between PYR and atoms of the active site during the MD.

Inline graphic — Ternary DlADH·NAD⁺·PYR complex with the ionization scenario of the catalytic triad after 5 ns of MD. (A) Amino acids lining the R1 (wire model in green) and R2 (wire model in blue) subpockets of the active site. The nicotinamide and ribose ring of NAD⁺, the catalytic triad (Ser-138, Tyr-151, and Lys-155), and PYR are shown as stick models with coloring according to the atom type (carbon-yellow, nitrogen-blue, oxygen-red, and hydrogen-gray). The ribbon represents the C-terminal loop of the other subunit acting as a lid of the active site cavity. PYR is shown both before and after the 5 ns of MD. The ring was parallel to the nicontinamide ring of the NAD⁺ ring at the start of the MD but tilted to perpendicular during the MD. (B) Fluctuation of atomic distances between PYR and atoms of the active site during the MD.