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. 2014 Jan 17;53(5):881–894. doi: 10.1021/bi401583f

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
a

Weighted average of the bond distances and errors for two subunits from refinement with SHELXL-2013 with no restraints on distances or planarity.

b

Ligand C is the “reactive” methylene carbon, C7 of benzyl alcohol and C1 (labeled C2 in the PDB entry) for TFE.

c

Angle between the C3–C4–C5 and C2–C3–C6 planes.105

d

Angle between the C2–N1–C6 and C2–C3–C6 planes.

e

Distortion of the boat conformation, defined as the distance between C5 and the C2–C3–C6 plane.