Fluorine in PDB 7uei: Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16

Enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16, PDB code: 7uei was solved by B.V.Plapp, L.Gakhar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.31, 51.27, 92.52, 91.9, 103.01, 110.12
R / Rfree (%) 12.7 / 15

Other elements in 7uei:

The structure of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 (pdb code 7uei). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16, PDB code: 7uei:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 7uei

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Fluorine binding site 1 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:13.6
occ:1.00
 F2 A:PFB404 0.0 13.6 1.0
C2 A:PFB404 1.3 12.3 1.0
C3 A:PFB404 2.3 13.6 1.0
C1 A:PFB404 2.4 11.8 1.0
F3 A:PFB404 2.6 14.5 1.0
C7N A:NAJ403 2.9 7.9 1.0
C7 A:PFB404 2.9 12.6 1.0
C3N A:NAJ403 3.0 8.9 1.0
O7N A:NAJ403 3.0 9.1 1.0
C2N A:NAJ403 3.4 8.0 1.0
N7N A:NAJ403 3.4 9.0 1.0
C4 A:PFB404 3.5 12.6 1.0
C6 A:PFB404 3.6 13.4 1.0
CD1 A:ILE318 3.7 15.9 1.0
O1 A:PFB404 3.8 11.1 1.0
C4N A:NAJ403 3.8 10.1 1.0
CG2 A:VAL294 3.8 10.2 0.6
CG2 A:VAL294 3.8 10.9 0.4
C5 A:PFB404 4.0 12.2 1.0
N1N A:NAJ403 4.3 8.1 1.0
CE1 A:PHE93 4.5 9.5 1.0
OG A:SER48 4.5 9.9 1.0
CG2 A:ILE318 4.6 10.5 1.0
CD2 A:LEU116 4.6 14.9 0.7
F4 A:PFB404 4.6 16.2 1.0
C5N A:NAJ403 4.7 9.5 1.0
CD1 A:LEU116 4.7 17.8 0.3
F6 A:PFB404 4.7 12.9 1.0
CD2 B:LEU309 4.7 13.4 0.7
CZ A:PHE93 4.8 10.1 1.0
C6N A:NAJ403 4.9 9.2 1.0
CG1 A:ILE318 4.9 11.1 1.0

Fluorine binding site 2 out of 10 in 7uei

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Fluorine binding site 2 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:14.5
occ:1.00
 F3 A:PFB404 0.0 14.5 1.0
C3 A:PFB404 1.3 13.6 1.0
C2 A:PFB404 2.3 12.3 1.0
C4 A:PFB404 2.3 12.6 1.0
F2 A:PFB404 2.6 13.6 1.0
F4 A:PFB404 2.7 16.2 1.0
CD2 A:LEU116 3.4 17.9 0.3
CG2 A:VAL294 3.5 10.9 0.4
CD1 A:ILE318 3.5 15.9 1.0
CG2 A:VAL294 3.5 10.2 0.6
C5 A:PFB404 3.6 12.2 1.0
C1 A:PFB404 3.6 11.8 1.0
CD2 B:LEU309 3.6 13.4 0.7
CD2 A:LEU116 3.7 14.9 0.7
CD1 A:LEU116 3.9 17.8 0.3
O A:HOH948 3.9 35.5 1.0
CG A:LEU116 3.9 18.3 0.3
C6 A:PFB404 4.1 13.4 1.0
CG1 A:VAL294 4.5 11.9 0.4
CB A:VAL294 4.6 10.7 0.4
F5 A:PFB404 4.7 14.5 1.0
CB A:VAL294 4.7 10.1 0.6
CG1 A:VAL294 4.8 10.6 0.6
CG A:LEU116 4.8 13.4 0.7
CG B:LEU309 4.8 11.7 0.7
CG1 A:ILE318 4.9 11.1 1.0
C7 A:PFB404 4.9 12.6 1.0
CE B:MET306 5.0 21.3 1.0

Fluorine binding site 3 out of 10 in 7uei

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Fluorine binding site 3 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:16.2
occ:1.00
 F4 A:PFB404 0.0 16.2 1.0
C4 A:PFB404 1.3 12.6 1.0
C3 A:PFB404 2.3 13.6 1.0
C5 A:PFB404 2.3 12.2 1.0
F3 A:PFB404 2.7 14.5 1.0
F5 A:PFB404 2.7 14.5 1.0
CD1 A:LEU57 3.2 18.0 0.3
CD2 A:LEU57 3.3 17.4 0.7
CG A:LEU116 3.4 18.3 0.3
C2 A:PFB404 3.5 12.3 1.0
CD2 A:LEU57 3.6 17.1 0.3
C6 A:PFB404 3.6 13.4 1.0
CD2 A:LEU116 3.7 17.9 0.3
O A:HOH948 3.7 35.5 1.0
CD1 A:LEU57 3.7 15.4 0.7
CD2 A:LEU116 3.9 14.9 0.7
O A:HOH779 3.9 44.7 1.0
CD1 A:LEU116 3.9 17.8 0.3
CG A:LEU57 4.0 15.1 0.3
CG A:LEU116 4.1 13.4 0.7
C1 A:PFB404 4.1 11.8 1.0
CG A:LEU57 4.1 14.7 0.7
CB A:LEU116 4.5 14.3 0.7
F2 A:PFB404 4.6 13.6 1.0
F6 A:PFB404 4.7 12.9 1.0
CB A:LEU116 4.7 18.2 0.3
CG2 A:VAL294 4.8 10.2 0.6
CG1 A:VAL294 4.8 11.9 0.4
O A:LEU116 4.8 22.9 1.0
CD2 A:LEU141 4.9 13.7 1.0
CG2 A:VAL294 4.9 10.9 0.4
CG1 A:VAL294 5.0 10.6 0.6
CA A:LEU116 5.0 15.0 0.3
CA A:LEU116 5.0 13.4 0.7

Fluorine binding site 4 out of 10 in 7uei

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Fluorine binding site 4 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:14.5
occ:1.00
 F5 A:PFB404 0.0 14.5 1.0
C5 A:PFB404 1.4 12.2 1.0
C4 A:PFB404 2.3 12.6 1.0
C6 A:PFB404 2.4 13.4 1.0
F6 A:PFB404 2.7 12.9 1.0
F4 A:PFB404 2.7 16.2 1.0
CD2 A:LEU57 2.7 17.1 0.3
CD1 A:LEU57 3.2 15.4 0.7
CZ A:PHE140 3.3 11.5 1.0
CD1 A:LEU141 3.4 11.5 1.0
C3 A:PFB404 3.6 13.6 1.0
C1 A:PFB404 3.6 11.8 1.0
CD2 A:LEU141 3.7 13.7 1.0
CE1 A:PHE140 3.7 12.2 1.0
CG A:LEU57 4.0 15.1 0.3
CG A:LEU141 4.0 11.3 1.0
C2 A:PFB404 4.1 12.3 1.0
CD1 A:LEU57 4.2 18.0 0.3
CE2 A:PHE140 4.3 11.7 1.0
CG A:LEU57 4.3 14.7 0.7
CD2 A:LEU57 4.4 17.4 0.7
CB A:SER48 4.4 10.4 1.0
F3 A:PFB404 4.7 14.5 1.0
CD1 A:LEU116 4.8 17.8 0.3
C7 A:PFB404 4.9 12.6 1.0
CG A:LEU116 4.9 13.4 0.7
CG A:LEU116 4.9 18.3 0.3
CD1 A:PHE140 4.9 10.3 1.0
CD2 A:LEU116 5.0 14.9 0.7
OG A:SER48 5.0 9.9 1.0

Fluorine binding site 5 out of 10 in 7uei

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Fluorine binding site 5 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:12.9
occ:1.00
 F6 A:PFB404 0.0 12.9 1.0
C6 A:PFB404 1.3 13.4 1.0
C5 A:PFB404 2.3 12.2 1.0
C1 A:PFB404 2.4 11.8 1.0
F5 A:PFB404 2.7 14.5 1.0
C7 A:PFB404 2.8 12.6 1.0
O1 A:PFB404 3.1 11.1 1.0
CB A:SER48 3.2 10.4 1.0
CD1 A:LEU141 3.2 11.5 1.0
NE2 A:HIS67 3.3 9.9 1.0
CE1 A:HIS67 3.4 9.5 1.0
CD2 A:HIS67 3.5 9.7 1.0
C4 A:PFB404 3.6 12.6 1.0
C2 A:PFB404 3.6 12.3 1.0
OG A:SER48 3.7 9.9 1.0
ND1 A:HIS67 3.7 10.1 1.0
CG A:HIS67 3.7 9.3 1.0
CZ A:PHE140 4.0 11.5 1.0
ZN A:ZN401 4.1 10.8 1.0
C3 A:PFB404 4.1 13.6 1.0
CE2 A:PHE140 4.3 11.7 1.0
CG A:LEU141 4.6 11.3 1.0
CA A:SER48 4.6 10.4 1.0
F4 A:PFB404 4.7 16.2 1.0
CB A:HIS67 4.7 10.0 1.0
F2 A:PFB404 4.7 13.6 1.0
CD1 A:LEU57 4.8 15.4 0.7
CD1 A:PHE93 4.8 9.3 1.0
CD2 A:LEU57 4.8 17.1 0.3
C A:SER48 4.8 9.9 1.0
CE1 A:PHE93 4.8 9.5 1.0

Fluorine binding site 6 out of 10 in 7uei

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Fluorine binding site 6 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:16.8
occ:1.00
 F2 B:PFB404 0.0 16.8 1.0
C2 B:PFB404 1.4 15.5 1.0
C3 B:PFB404 2.4 15.5 1.0
C1 B:PFB404 2.4 15.7 1.0
F3 B:PFB404 2.7 17.1 1.0
C7N B:NAJ403 2.9 10.7 1.0
C7 B:PFB404 2.9 14.5 1.0
O7N B:NAJ403 3.0 11.7 1.0
C3N B:NAJ403 3.0 10.8 1.0
C2N B:NAJ403 3.4 10.3 1.0
N7N B:NAJ403 3.5 11.4 1.0
CG2 B:VAL294 3.5 15.4 0.5
C4 B:PFB404 3.6 17.4 1.0
C6 B:PFB404 3.6 14.3 1.0
O1 B:PFB404 3.7 13.6 1.0
CD1 B:ILE318 3.7 17.9 1.0
C4N B:NAJ403 3.8 12.6 1.0
CG2 B:VAL294 4.0 12.6 0.5
C5 B:PFB404 4.1 16.4 1.0
N1N B:NAJ403 4.3 11.1 1.0
OG B:SER48 4.4 12.4 1.0
CE1 B:PHE93 4.5 12.8 1.0
CD1 B:LEU116 4.5 21.2 0.4
F4 B:PFB404 4.6 18.7 1.0
CG2 B:ILE318 4.6 12.8 1.0
CD2 B:LEU116 4.7 20.1 0.6
C5N B:NAJ403 4.7 11.6 1.0
F6 B:PFB404 4.7 15.8 1.0
CD2 A:LEU309 4.8 15.4 0.7
CZ B:PHE93 4.8 12.7 1.0
C6N B:NAJ403 4.9 11.8 1.0
CG1 B:ILE318 5.0 13.3 1.0

Fluorine binding site 7 out of 10 in 7uei

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Fluorine binding site 7 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:17.1
occ:1.00
 F3 B:PFB404 0.0 17.1 1.0
C3 B:PFB404 1.3 15.5 1.0
C2 B:PFB404 2.3 15.5 1.0
C4 B:PFB404 2.4 17.4 1.0
F2 B:PFB404 2.7 16.8 1.0
F4 B:PFB404 2.7 18.7 1.0
CG2 B:VAL294 3.3 15.4 0.5
CD2 B:LEU116 3.5 20.3 0.4
CD1 B:ILE318 3.6 17.9 1.0
CG2 B:VAL294 3.6 12.6 0.5
C5 B:PFB404 3.6 16.4 1.0
C1 B:PFB404 3.6 15.7 1.0
CD2 A:LEU309 3.7 15.4 0.7
CD2 B:LEU116 3.7 20.1 0.6
CD1 B:LEU116 3.7 21.2 0.4
CG B:LEU116 4.0 18.4 0.4
C6 B:PFB404 4.1 14.3 1.0
CG1 B:VAL294 4.3 14.7 0.5
CB B:VAL294 4.4 13.9 0.5
F5 B:PFB404 4.7 17.4 1.0
CG A:LEU309 4.8 13.6 0.7
CG B:LEU116 4.8 16.4 0.6
CB B:VAL294 4.9 10.7 0.5
C7 B:PFB404 4.9 14.5 1.0
CG1 B:VAL294 4.9 11.2 0.5
CG1 B:ILE318 4.9 13.3 1.0

Fluorine binding site 8 out of 10 in 7uei

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Fluorine binding site 8 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:18.7
occ:1.00
 F4 B:PFB404 0.0 18.7 1.0
C4 B:PFB404 1.3 17.4 1.0
C3 B:PFB404 2.3 15.5 1.0
C5 B:PFB404 2.3 16.4 1.0
F3 B:PFB404 2.7 17.1 1.0
F5 B:PFB404 2.7 17.4 1.0
CD2 B:LEU57 3.4 22.6 1.0
CG B:LEU116 3.4 18.4 0.4
CD2 B:LEU116 3.5 20.3 0.4
C2 B:PFB404 3.5 15.5 1.0
C6 B:PFB404 3.6 14.3 1.0
CD1 B:LEU57 3.6 22.8 1.0
O B:HOH743 3.7 35.1 1.0
CD1 B:LEU116 3.8 21.2 0.4
CD2 B:LEU116 4.0 20.1 0.6
C1 B:PFB404 4.1 15.7 1.0
CG B:LEU57 4.1 23.1 1.0
CG B:LEU116 4.2 16.4 0.6
CG1 B:VAL294 4.6 14.7 0.5
F2 B:PFB404 4.6 16.8 1.0
CB B:LEU116 4.7 18.5 0.6
F6 B:PFB404 4.7 15.8 1.0
O B:LEU116 4.7 22.6 0.4
CG2 B:VAL294 4.7 15.4 0.5
CB B:LEU116 4.8 17.4 0.4
CG2 B:VAL294 4.9 12.6 0.5

Fluorine binding site 9 out of 10 in 7uei

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Fluorine binding site 9 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:17.4
occ:1.00
 F5 B:PFB404 0.0 17.4 1.0
C5 B:PFB404 1.3 16.4 1.0
C4 B:PFB404 2.3 17.4 1.0
C6 B:PFB404 2.3 14.3 1.0
F6 B:PFB404 2.7 15.8 1.0
F4 B:PFB404 2.7 18.7 1.0
CD1 B:LEU57 3.1 22.8 1.0
CZ B:PHE140 3.3 15.4 1.0
CD1 B:LEU141 3.4 14.9 1.0
C3 B:PFB404 3.6 15.5 1.0
C1 B:PFB404 3.6 15.7 1.0
CD2 B:LEU141 3.8 18.0 1.0
CE1 B:PHE140 3.8 15.5 1.0
CG B:LEU141 4.0 14.3 1.0
C2 B:PFB404 4.0 15.5 1.0
CE2 B:PHE140 4.3 15.1 1.0
CG B:LEU57 4.4 23.1 1.0
CB B:SER48 4.4 11.9 1.0
O B:HOH743 4.5 35.1 1.0
CD2 B:LEU57 4.6 22.6 1.0
CD1 B:LEU116 4.7 21.2 0.4
F3 B:PFB404 4.7 17.1 1.0
CG B:LEU116 4.7 18.4 0.4
O B:HOH590 4.8 29.6 1.0
C7 B:PFB404 4.8 14.5 1.0
CG B:LEU116 4.9 16.4 0.6
O B:SER48 5.0 14.7 1.0
OG B:SER48 5.0 12.4 1.0
CD1 B:PHE140 5.0 14.6 1.0

Fluorine binding site 10 out of 10 in 7uei

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Fluorine binding site 10 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 100 K, 1.2 A, Crystal 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:15.8
occ:1.00
 F6 B:PFB404 0.0 15.8 1.0
C6 B:PFB404 1.3 14.3 1.0
C1 B:PFB404 2.3 15.7 1.0
C5 B:PFB404 2.3 16.4 1.0
F5 B:PFB404 2.7 17.4 1.0
C7 B:PFB404 2.8 14.5 1.0
O1 B:PFB404 3.1 13.6 1.0
CD1 B:LEU141 3.2 14.9 1.0
CB B:SER48 3.2 11.9 1.0
NE2 B:HIS67 3.3 12.8 1.0
CE1 B:HIS67 3.4 12.1 1.0
CD2 B:HIS67 3.5 12.5 1.0
C4 B:PFB404 3.6 17.4 1.0
C2 B:PFB404 3.6 15.5 1.0
ND1 B:HIS67 3.7 12.2 1.0
OG B:SER48 3.7 12.4 1.0
CG B:HIS67 3.7 11.8 1.0
ZN B:ZN401 4.1 13.5 1.0
C3 B:PFB404 4.1 15.5 1.0
CZ B:PHE140 4.1 15.4 1.0
CE2 B:PHE140 4.3 15.1 1.0
CA B:SER48 4.6 12.2 1.0
CG B:LEU141 4.6 14.3 1.0
F4 B:PFB404 4.7 18.7 1.0
CB B:HIS67 4.7 12.9 1.0
F2 B:PFB404 4.7 16.8 1.0
C B:SER48 4.8 13.7 1.0
CD1 B:PHE93 4.8 11.9 1.0
CE1 B:PHE93 4.8 12.8 1.0
CD1 B:LEU57 4.9 22.8 1.0
O B:SER48 5.0 14.7 1.0

Reference:

B.V.Plapp, L.Gakhar, R.Subramanian. Dependence of Crystallographic Atomic Displacement Factors on Temperature (25-150 K) For Complexes of Horse Liver Alcohol Dehydrogenases Acta Crystallogr.,Sect.D V. D78 1221 2022.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798322008361
Page generated: Fri Aug 2 14:08:39 2024

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