PMC

Alternative conformation for Lys-228 and its accompanying water. The green stick model and water represent the alternative positions. Hydrogen bonds are represented by the dashed lines. The electron density map is contoured at about 1 σ above the mean.

Electron density maps for complexes of ADH with NAD⁺ and the fluoroalcohols. Interactions in the proton relay system shown in dashed lines. The dotted line with label 3.4 Å shows the distance between C4N of the nicotinamide ring and the methylene carbon of the alcohol. The stereoviews are rotated about 180° in order to see different views. (A) Binding of pentafluorobenzyl alcohol. Electron density is at about 4 σ above the mean. (B) Binding of trifluoroethanol. Electron density is at about 4.9 σ above the mean.

Interactions of alcohols with active site residues. The coordination of the catalytic zinc ion and the hydrogen bonds of the alcohol in the proton relay system are shown as dotted lines. The riding hydrogens of the methylene carbons are shown in cyan and the other atoms have usual atomic coloring, except that the alternative conformations of the side chains of Leu-57 and Leu-309B (other subunit) are shown in green. Note that the conformations of Leu-57 and Leu-116 differ in the two structures. (A) Pentafluorobenzyl alcohol. (B) Trifluoroethanol.

Puckering of the nicotinamide rings. (A) The structure of the complex with NAD⁺ and TFE (subunit A) is shown with atoms C2N and C3N aligned on top of atoms C5N and C6N so that the displacements of N1N and C4N from the plane are visible. (B) Comparison of the structure of the complex with NAD⁺ and pentafluorobenzyl alcohol to that with NADH and methylhexylformamide. The “A” subunits of the structures (amino acid residues A1 to A374) were superimposed, with an rmsd of 0.25 Å. The complex with NAD⁺ and pentafluorobenzyl alcohol (with H atoms in magenta but F atoms removed for clarity) are shown in atom coloring with ball and stick representation. The complex with NADH (with H atoms on C4N) and methylhexylformamide (“MHF”, with atoms C3-C6 removed for clarity) is shown in green. The residues making close contacts are labeled. The distances are given in .