Table 2. Nicotinamide Ring Puckering in Complexes of Horse Liver ADHa.
| ligands | PDB entries | α-C4 (deg) | α-N1 (deg) | twist (Å) |
|---|---|---|---|---|
| NADH, H2Ob | 4XD2 | 16.0 ± 1.6 | 12.6 ± 2.2 | –0.26 ± 0.03 |
| NADH, MHFc | 1P1R, 5VN1 | 18.1 ± 4.2 | 11.2 ± 2.3 | –0.04 ± 0.12 |
| NADH, BNFd | 5VL0 | 12.5 ± 3.9 | 13.1 ± 3.2 | 0.07 ± 0.07 |
| NADH, variouse | 1HET, 2JHG | 12.3 ± 2.5 | 11.0 ± 4.5 | –0.31 ± 0.19 |
| NAD+, FALCf | 4DXH, 4DWV | 4.9 ± 2.3 | 5.8 ± 2.1 | 0.06 ± 0.03 |
The structures were refined with relaxed or no restraints on the nicotinamide ring. Ring puckering geometry is defined as follows: α-C4, angle between the C3–C4–C5 and C2–C3–C6 planes; α-N1, angle between the C2–N1–C6 and C2–C3–C6 planes; twist, distortion of the boat conformation, defined as the distance between C5 and the C2–C3–C6 plane.22
Weighted average from two subunits as calculated with SHELXL-2013 with no restraints on the nicotinamide ring.
Average of eight subunits of the enzyme complexed with NADH and N-1-methylhexylformamide, an aldehyde analogue and potent inhibitor,11 calculated with SHELXL-2013 after refinement with REFMAC.
Average of four subunits of the enzyme complexed with NADH and N-benzylformamide calculated with SHELXL-2013 after refinement with REFMAC.
Average of eight subunits from four structures of wild-type ADH with Zn(II) or Cd(II) at the active sites, complexed with NADH and other ligands, including water, methylpentanediol, dimethyl sulfoxide, or isobutyramide (PDB entries 1HEU, 2JHF, 1HET, and 2JHG).22,23
Weighted average of four subunits of the enzyme complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol calculated with SHELXL-2013 with no restraints on the nicotinamide ring.62