Table 4. Bond Distances and Geometry of Ligands in the Active Site.
| average
bond distances (Å) in the nicotinamide
ringa |
||||||
|---|---|---|---|---|---|---|
| structure, PDB entry | N1–C2 | C2–C3 | C3–C4 | C4–C5 | C5–C6 | C6–N1 |
| WT–PFB, 4DWV | 1.345 ± 0.011 | 1.338 ± 0.013 | 1.445 ± 0.014 | 1.396 ± 0.015 | 1.356 ± 0.015 | 1.392 ± 0.012 |
| WT–TFE, 4DXH | 1.366 ± 0.012 | 1.379 ± 0.014 | 1.404 ± 0.014 | 1.366 ± 0.014 | 1.382 ± 0.015 | 1.380 ± 0.012 |
| 207A–PFB, 4NFH | 1.373 ± 0.015 | 1.335 ± 0.019 | 1.431 ± 0.021 | 1.400 ± 0.021 | 1.368 ± 0.020 | 1.403 ± 0.017 |
| 203A–PFB, 4NG5 | 1.373 ± 0.011 | 1.362 ± 0.013 | 1.437 ± 0.015 | 1.443 ± 0.016 | 1.335 ± 0.015 | 1.405 ± 0.012 |
| 203A–TFE, 4NFS | 1.334 ± 0.013 | 1.327 ± 0.015 | 1.476 ± 0.017 | 1.402 ± 0.019 | 1.358 ± 0.017 | 1.407 ± 0.015 |
| ligand
distances (Å) |
nicotinamide
ring pucker |
|||||
|---|---|---|---|---|---|---|
| NAD C4N–ligand Cb | Zn–ligand O1 | O1–OG 48 | α-C4 (deg)c | α-N1 (deg)d | twist (Å)e | |
| WT–PFB | 3.37 ± 0.02 | 1.96 ± 0.01 | 2.50 ± 0.01 | 5.6 ± 1.5 | 3.7 ± 1.5 | 0.038 ± 0.021 |
| WT–TFE | 3.44 ± 0.02 | 1.96 ± 0.01 | 2.45 ± 0.01 | 5.6 ± 1.6 | 3.9 ± 1.5 | 0.047 ± 0.020 |
| 207A–PFB | 3.29 ± 0.02 | 2.00 ± 0.01 | 2.42 ± 0.02 | 4.9 ± 2.3 | 5.8 ± 2.1 | 0.056 ± 0.030 |
| 203A–PFB | 3.40 ± 0.02 | 1.94 ± 0.01 | 2.52 ± 0.02 | 8.4 ± 1.4 | 8.0 ± 1.2 | 0.054 ± 0.018 |
| 203A–TFE | 3.53 ± 0.03 | 2.00 ± 0.01 | 2.60 ± 0.02 | 12.6 ± 1.6 | 8.0 ± 1.7 | 0.037 ± 0.024 |
Weighted average of the bond distances and errors for two subunits from refinement with SHELXL-2013 with no restraints on distances or planarity.
Ligand C is the “reactive” methylene carbon, C7 of benzyl alcohol and C1 (labeled C2 in the PDB entry) for TFE.
Angle between the C3–C4–C5 and C2–C3–C6 planes.105
Angle between the C2–N1–C6 and C2–C3–C6 planes.
Distortion of the boat conformation, defined as the distance between C5 and the C2–C3–C6 plane.