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. Author manuscript; available in PMC: 2013 May 15.
Published in final edited form as: Biochemistry. 2012 May 1;51(19):4035–4048. doi: 10.1021/bi300378n

Table 4.

Bond distances (Å units) in Nicotinamide Rings

Structure N1-C2 C2-C3 C3-C4 C4-C5 C5-C6 C6-N1 average deviation
1 PFB, A subunita 1.365 ± 0.011 1.362 ± 0.012 1.441 ± 0.013 1.415 ± 0.014 1.358 ± 0.013 1.420 ± 0.012 0.012
2 PFB, B subunita 1.375 ± 0.024 1.353 ± 0.033 1.443 ± 0.018 1.394 ± 0.034 1.352 ± 0.034 1.391 ± 0.015 0.026
3 TFE, A subunita 1.378 ± 0.013 1.365 ± 0.014 1.416 ± 0.017 1.371 ± 0.016 1.371 ± 0.014 1.398 ± 0.014 0.015
4 TFE, B subunita 1.384 ± 0.087 1.354 ± 0.128 1.408 ± 0.026 1.376 ± 0.123 1.365 ± 0.123 1.389 ± 0.026 0.086
5 Weighted average of 4 subunitsa 1.371 ± 0.008 1.363 ± 0.009 1.432 ± 0.009 1.396 ± 0.010 1.363 ± 0.009 1.404 ± 0.007 0.009
6 REFMAC, averageb 1.37 1.35 1.43 1.38 1.36 1.38 0.018
7 NAJc 1.346 1.391 1.398 1.384 1.379 1.347 0.005
8 LiNAD+d 1.39 1.37 1.40 1.42 1.37 1.35 0.02
9 NAD(P)+e 1.36 1.38 1.40 1.39 1.38 1.37 0.014
10 dihydronicotinamidef 1.38 1.32 1.51 1.53 1.32 1.43 0.012
11 NADH, as NAJg 1.40 1.38 1.50 1.46 1.36 1.46 0.034
12 NADH in ADHh 1.40 1.35 1.48 1.47 1.41 1.40 0.031
13 NADPHi 1.38 1.38 1.49 1.48 1.38 1.42 0.026
a

Bond distances and errors from refinement with SHELXL with no restraints on the bond distances and planarity for the coenzyme.

b

Average bond distances (of 4 subunits) from refinement of PFB and TFE structures with REFMAC with relaxed restraints (0.10 Å) on distances and no restraints on planarity of the nicotinamide ring. (Note that protons were removed on N1A and phosphate AO2 to represent the coenzyme at neutral pH).

c

Neutron diffraction at 0.65 Å resolution with estimated errors of 0.005 Å.64

d

X-ray data at 1.09 Å with estimated average errors of 0.02 Å.89 The distances are within 0.03 Å of those found for N-1-(2,6-dichlorobenzyl)-3-carbamidopyridinium iodide.90

e

Five structures of enzymes complexed with NAD+ determined at 1.0 – 1.2 Å resolution (PDB entries: 1ZJZ, 1SBY, 1T2D, 3JY0, 2O23) and five structures with NADP+ determined at 0.66 to 1.0 Å resolution (PDB entries: 1US0, 3BCJ, 1PWM, 2J8T, 1ZK4). These values are within 0.01 Å of the target values in the dictionary from REFMAC where the restraints usually are set at 0.02 Å.

f

N-Benzyl-1,4-dihydronicotinamide.91 The nicotinamide ring is planar.

g

Average of eight subunits in complexes of ADH with NADH, refined as NAJ, and (R)-N-1-methylhexylformamide (1.57 Å resolution, 1P1R.pdb66) or (1S,3S)-3-butylthiolane 1-oxide (1.66 Å resolution, 3BTO.pdb37).

h

Four structures (1.0 – 1.2 Å, average of 8 subunits) of zinc or cadmium horse liver ADH complexed with NADH and isobutyramide, dimethyl sulfoxide, or hydroxide partly adducted to the nicotinamide ring (PDB files: 1HET, 1HEU, 2JHG, 1JHF).20,21

i

Five structures of NADPH in enzymes determined at 1.09 to 1.35 Å resolution; all nicotinamide rings were essentially planar (PDB files: 3DJJ, 1LQU, 1YNQ, 1HEJ, 1KMS).