Fluorine in PDB 7udr: Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K

Enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K, PDB code: 7udr 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) 19.81 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.42, 51.21, 92.41, 91.72, 103.12, 110.22
R / Rfree (%) 12.4 / 15.9

Other elements in 7udr:

The structure of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K 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 25 K (pdb code 7udr). 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 25 K, PDB code: 7udr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 7udr

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Fluorine binding site 1 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K


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 25 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:15.1
occ:1.00
 F2 A:PFB404 0.0 15.1 1.0
C2 A:PFB404 1.3 13.4 1.0
C3 A:PFB404 2.3 14.1 1.0
C1 A:PFB404 2.4 13.7 1.0
F3 A:PFB404 2.7 14.9 1.0
C7N A:NAJ403 2.8 10.2 1.0
C7 A:PFB404 2.9 12.9 1.0
C3N A:NAJ403 2.9 11.0 1.0
O7N A:NAJ403 3.0 10.7 1.0
C2N A:NAJ403 3.3 9.7 1.0
N7N A:NAJ403 3.4 10.1 1.0
C4 A:PFB404 3.5 15.5 1.0
C6 A:PFB404 3.6 14.9 1.0
CD1 A:ILE318 3.7 17.0 1.0
CG2 A:VAL294 3.7 11.9 0.4
CG2 A:VAL294 3.8 12.4 0.6
C4N A:NAJ403 3.8 12.0 1.0
O1 A:PFB404 3.8 13.2 1.0
C5 A:PFB404 4.0 15.0 1.0
N1N A:NAJ403 4.2 9.6 1.0
OG A:SER48 4.5 11.5 1.0
CE1 A:PHE93 4.5 10.6 1.0
CG2 A:ILE318 4.6 11.6 1.0
C5N A:NAJ403 4.6 10.2 1.0
F4 A:PFB404 4.7 19.6 1.0
CD2 A:LEU116 4.7 16.8 0.7
CD1 A:LEU116 4.7 17.0 0.3
CD2 B:LEU309 4.7 15.6 0.7
F6 A:PFB404 4.7 14.6 1.0
CZ A:PHE93 4.8 11.3 1.0
C6N A:NAJ403 4.9 10.4 1.0
CG1 A:ILE318 4.9 13.0 1.0

Fluorine binding site 2 out of 10 in 7udr

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Fluorine binding site 2 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K


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 25 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:14.9
occ:1.00
 F3 A:PFB404 0.0 14.9 1.0
C3 A:PFB404 1.3 14.1 1.0
C4 A:PFB404 2.3 15.5 1.0
C2 A:PFB404 2.3 13.4 1.0
F2 A:PFB404 2.7 15.1 1.0
F4 A:PFB404 2.7 19.6 1.0
CG2 A:VAL294 3.4 11.9 0.4
CD2 A:LEU116 3.4 16.5 0.3
CG2 A:VAL294 3.5 12.4 0.6
CD1 A:ILE318 3.5 17.0 1.0
C5 A:PFB404 3.5 15.0 1.0
C1 A:PFB404 3.6 13.7 1.0
CD2 B:LEU309 3.7 15.6 0.7
CD2 A:LEU116 3.7 16.8 0.7
CD1 A:LEU116 3.9 17.0 0.3
CG A:LEU116 4.0 16.9 0.3
O A:HOH948 4.0 38.2 1.0
C6 A:PFB404 4.0 14.9 1.0
CG1 A:VAL294 4.4 12.8 0.4
CB A:VAL294 4.6 11.0 0.4
CB A:VAL294 4.6 12.5 0.6
F5 A:PFB404 4.7 16.4 1.0
CG1 A:VAL294 4.7 12.9 0.6
CG B:LEU309 4.8 12.4 0.7
CG A:LEU116 4.8 15.2 0.7
CG1 A:ILE318 4.9 13.0 1.0
C7 A:PFB404 4.9 12.9 1.0
CE B:MET306 5.0 24.0 1.0
O A:HOH733 5.0 48.8 1.0

Fluorine binding site 3 out of 10 in 7udr

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Fluorine binding site 3 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K


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 25 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:19.6
occ:1.00
 F4 A:PFB404 0.0 19.6 1.0
C4 A:PFB404 1.4 15.5 1.0
C5 A:PFB404 2.3 15.0 1.0
C3 A:PFB404 2.4 14.1 1.0
F3 A:PFB404 2.7 14.9 1.0
F5 A:PFB404 2.7 16.4 1.0
CD1 A:LEU57 3.1 17.7 0.3
CD2 A:LEU57 3.3 18.1 0.7
CG A:LEU116 3.3 16.9 0.3
CD2 A:LEU116 3.4 16.5 0.3
C2 A:PFB404 3.6 13.4 1.0
C6 A:PFB404 3.6 14.9 1.0
O A:HOH733 3.6 48.8 1.0
O A:HOH948 3.7 38.2 1.0
CD2 A:LEU57 3.7 20.2 0.3
CD1 A:LEU57 3.8 16.0 0.7
CD1 A:LEU116 3.8 17.0 0.3
CD2 A:LEU116 3.9 16.8 0.7
CG A:LEU57 4.0 16.4 0.3
CG A:LEU57 4.1 16.0 0.7
CG A:LEU116 4.1 15.2 0.7
C1 A:PFB404 4.1 13.7 1.0
CB A:LEU116 4.5 16.4 0.7
F2 A:PFB404 4.7 15.1 1.0
CB A:LEU116 4.7 19.1 0.3
F6 A:PFB404 4.7 14.6 1.0
CG2 A:VAL294 4.7 12.4 0.6
O A:LEU116 4.8 24.6 1.0
CG1 A:VAL294 4.8 12.8 0.4
CD2 A:LEU141 4.9 17.1 1.0
CG2 A:VAL294 4.9 11.9 0.4
CG1 A:VAL294 4.9 12.9 0.6
CA A:LEU116 5.0 16.1 0.3

Fluorine binding site 4 out of 10 in 7udr

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Fluorine binding site 4 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K


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 25 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:16.4
occ:1.00
 F5 A:PFB404 0.0 16.4 1.0
C5 A:PFB404 1.4 15.0 1.0
C4 A:PFB404 2.3 15.5 1.0
C6 A:PFB404 2.4 14.9 1.0
F4 A:PFB404 2.7 19.6 1.0
F6 A:PFB404 2.7 14.6 1.0
CD2 A:LEU57 2.8 20.2 0.3
CD1 A:LEU57 3.2 16.0 0.7
CZ A:PHE140 3.3 12.7 1.0
CD1 A:LEU141 3.3 13.5 1.0
C3 A:PFB404 3.6 14.1 1.0
C1 A:PFB404 3.6 13.7 1.0
CD2 A:LEU141 3.6 17.1 1.0
CE1 A:PHE140 3.7 13.2 1.0
CG A:LEU141 3.9 12.3 1.0
CG A:LEU57 4.0 16.4 0.3
C2 A:PFB404 4.1 13.4 1.0
CD1 A:LEU57 4.1 17.7 0.3
CE2 A:PHE140 4.3 13.4 1.0
CG A:LEU57 4.3 16.0 0.7
CD2 A:LEU57 4.4 18.1 0.7
CB A:SER48 4.4 11.4 1.0
CD1 A:LEU116 4.6 17.0 0.3
F3 A:PFB404 4.7 14.9 1.0
CG A:LEU116 4.7 16.9 0.3
CG A:LEU116 4.9 15.2 0.7
C7 A:PFB404 4.9 12.9 1.0
CD2 A:LEU116 5.0 16.8 0.7
CD1 A:PHE140 5.0 12.3 1.0
OG A:SER48 5.0 11.5 1.0

Fluorine binding site 5 out of 10 in 7udr

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Fluorine binding site 5 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K


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 25 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:14.6
occ:1.00
 F6 A:PFB404 0.0 14.6 1.0
C6 A:PFB404 1.4 14.9 1.0
C5 A:PFB404 2.3 15.0 1.0
C1 A:PFB404 2.4 13.7 1.0
F5 A:PFB404 2.7 16.4 1.0
C7 A:PFB404 2.8 12.9 1.0
CD1 A:LEU141 3.2 13.5 1.0
O1 A:PFB404 3.2 13.2 1.0
CB A:SER48 3.2 11.4 1.0
NE2 A:HIS67 3.3 11.6 1.0
CE1 A:HIS67 3.4 11.3 1.0
CD2 A:HIS67 3.5 10.8 1.0
C4 A:PFB404 3.6 15.5 1.0
C2 A:PFB404 3.6 13.4 1.0
OG A:SER48 3.7 11.5 1.0
ND1 A:HIS67 3.7 11.4 1.0
CG A:HIS67 3.7 11.1 1.0
CZ A:PHE140 4.1 12.7 1.0
ZN A:ZN401 4.1 12.7 1.0
C3 A:PFB404 4.1 14.1 1.0
CE2 A:PHE140 4.3 13.4 1.0
CG A:LEU141 4.5 12.3 1.0
CA A:SER48 4.6 11.1 1.0
F4 A:PFB404 4.7 19.6 1.0
CB A:HIS67 4.7 11.3 1.0
CD1 A:PHE93 4.7 10.6 1.0
F2 A:PFB404 4.7 15.1 1.0
CE1 A:PHE93 4.8 10.6 1.0
CD1 A:LEU57 4.8 16.0 0.7
C A:SER48 4.8 12.0 1.0
CD2 A:LEU57 4.9 20.2 0.3
CD2 A:LEU141 5.0 17.1 1.0

Fluorine binding site 6 out of 10 in 7udr

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Fluorine binding site 6 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K


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 25 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:18.4
occ:1.00
 F2 B:PFB404 0.0 18.4 1.0
C2 B:PFB404 1.3 17.3 1.0
C3 B:PFB404 2.3 15.6 1.0
C1 B:PFB404 2.4 17.4 1.0
F3 B:PFB404 2.7 17.2 1.0
C7N B:NAJ403 2.8 11.4 1.0
C7 B:PFB404 2.9 15.1 1.0
C3N B:NAJ403 3.0 11.4 1.0
O7N B:NAJ403 3.1 12.9 1.0
C2N B:NAJ403 3.3 11.4 1.0
N7N B:NAJ403 3.4 11.9 1.0
CG2 B:VAL294 3.5 14.1 0.5
C4 B:PFB404 3.6 18.6 1.0
C6 B:PFB404 3.6 16.4 1.0
CD1 B:ILE318 3.7 18.4 1.0
O1 B:PFB404 3.8 14.3 1.0
C4N B:NAJ403 3.8 13.7 1.0
CG2 B:VAL294 3.9 15.2 0.5
C5 B:PFB404 4.1 19.0 1.0
N1N B:NAJ403 4.3 11.5 1.0
OG B:SER48 4.4 13.6 1.0
CD1 B:LEU116 4.5 20.7 0.4
CE1 B:PHE93 4.6 13.6 1.0
F4 B:PFB404 4.6 22.0 1.0
CG2 B:ILE318 4.6 14.0 1.0
C5N B:NAJ403 4.7 12.8 1.0
CD2 B:LEU116 4.7 20.3 0.6
F6 B:PFB404 4.7 16.8 1.0
CD2 A:LEU309 4.7 17.3 0.7
CZ B:PHE93 4.8 14.8 1.0
C6N B:NAJ403 4.9 12.9 1.0
CG1 B:ILE318 4.9 14.2 1.0
CB B:VAL294 5.0 14.0 0.5

Fluorine binding site 7 out of 10 in 7udr

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Fluorine binding site 7 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K


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 25 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:17.2
occ:1.00
 F3 B:PFB404 0.0 17.2 1.0
C3 B:PFB404 1.4 15.6 1.0
C2 B:PFB404 2.4 17.3 1.0
C4 B:PFB404 2.4 18.6 1.0
F4 B:PFB404 2.7 22.0 1.0
F2 B:PFB404 2.7 18.4 1.0
CG2 B:VAL294 3.3 14.1 0.5
CG2 B:VAL294 3.5 15.2 0.5
CD2 B:LEU116 3.5 20.6 0.4
C5 B:PFB404 3.6 19.0 1.0
CD1 B:ILE318 3.6 18.4 1.0
C1 B:PFB404 3.7 17.4 1.0
CD2 A:LEU309 3.7 17.3 0.7
CD1 B:LEU116 3.7 20.7 0.4
CD2 B:LEU116 3.8 20.3 0.6
CG B:LEU116 4.0 17.9 0.4
C6 B:PFB404 4.1 16.4 1.0
CG1 B:VAL294 4.1 13.4 0.5
CB B:VAL294 4.3 14.0 0.5
F5 B:PFB404 4.7 19.2 1.0
CB B:VAL294 4.8 12.0 0.5
CG A:LEU309 4.8 14.8 0.7
CG1 B:VAL294 4.8 13.7 0.5
CG B:LEU116 4.9 17.7 0.6
CG1 B:ILE318 4.9 14.2 1.0
C7 B:PFB404 5.0 15.1 1.0

Fluorine binding site 8 out of 10 in 7udr

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Fluorine binding site 8 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K


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 25 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:22.0
occ:1.00
 F4 B:PFB404 0.0 22.0 1.0
C4 B:PFB404 1.3 18.6 1.0
C3 B:PFB404 2.3 15.6 1.0
C5 B:PFB404 2.3 19.0 1.0
F3 B:PFB404 2.7 17.2 1.0
F5 B:PFB404 2.7 19.2 1.0
CD2 B:LEU57 3.3 22.8 1.0
CG B:LEU116 3.4 17.9 0.4
CD2 B:LEU116 3.5 20.6 0.4
C2 B:PFB404 3.6 17.3 1.0
C6 B:PFB404 3.6 16.4 1.0
CD1 B:LEU57 3.6 26.1 1.0
O B:HOH751 3.8 36.8 1.0
CD1 B:LEU116 3.8 20.7 0.4
CD2 B:LEU116 4.0 20.3 0.6
CG B:LEU57 4.1 25.4 1.0
C1 B:PFB404 4.1 17.4 1.0
CG B:LEU116 4.2 17.7 0.6
CG1 B:VAL294 4.5 13.4 0.5
CB B:LEU116 4.6 17.7 0.6
F2 B:PFB404 4.6 18.4 1.0
F6 B:PFB404 4.7 16.8 1.0
O B:LEU116 4.7 23.4 0.4
CG2 B:VAL294 4.8 14.1 0.5
CB B:LEU116 4.8 21.0 0.4
CG2 B:VAL294 4.9 15.2 0.5
CD2 B:LEU141 5.0 19.6 1.0

Fluorine binding site 9 out of 10 in 7udr

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Fluorine binding site 9 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K


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 25 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:19.2
occ:1.00
 F5 B:PFB404 0.0 19.2 1.0
C5 B:PFB404 1.3 19.0 1.0
C4 B:PFB404 2.3 18.6 1.0
C6 B:PFB404 2.4 16.4 1.0
F6 B:PFB404 2.7 16.8 1.0
F4 B:PFB404 2.7 22.0 1.0
CD1 B:LEU57 3.2 26.1 1.0
CZ B:PHE140 3.3 16.7 1.0
CD1 B:LEU141 3.4 15.5 1.0
C3 B:PFB404 3.6 15.6 1.0
C1 B:PFB404 3.6 17.4 1.0
CD2 B:LEU141 3.7 19.6 1.0
CE1 B:PHE140 3.8 15.8 1.0
CG B:LEU141 4.0 14.6 1.0
C2 B:PFB404 4.1 17.3 1.0
CE2 B:PHE140 4.2 16.9 1.0
CB B:SER48 4.4 13.3 1.0
CG B:LEU57 4.4 25.4 1.0
O B:HOH751 4.5 36.8 1.0
CD2 B:LEU57 4.5 22.8 1.0
CD1 B:LEU116 4.7 20.7 0.4
F3 B:PFB404 4.7 17.2 1.0
CG B:LEU116 4.7 17.9 0.4
O B:HOH592 4.8 31.9 1.0
C7 B:PFB404 4.9 15.1 1.0
CG B:LEU116 4.9 17.7 0.6
OG B:SER48 5.0 13.6 1.0
CD1 B:PHE140 5.0 15.2 1.0
O B:SER48 5.0 15.6 1.0

Fluorine binding site 10 out of 10 in 7udr

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Fluorine binding site 10 out of 10 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 25 K


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 25 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:16.8
occ:1.00
 F6 B:PFB404 0.0 16.8 1.0
C6 B:PFB404 1.3 16.4 1.0
C5 B:PFB404 2.3 19.0 1.0
C1 B:PFB404 2.3 17.4 1.0
F5 B:PFB404 2.7 19.2 1.0
C7 B:PFB404 2.8 15.1 1.0
O1 B:PFB404 3.2 14.3 1.0
CD1 B:LEU141 3.2 15.5 1.0
CB B:SER48 3.2 13.3 1.0
NE2 B:HIS67 3.3 13.8 1.0
CE1 B:HIS67 3.4 13.0 1.0
CD2 B:HIS67 3.5 13.2 1.0
C4 B:PFB404 3.5 18.6 1.0
C2 B:PFB404 3.6 17.3 1.0
OG B:SER48 3.7 13.6 1.0
ND1 B:HIS67 3.7 13.1 1.0
CG B:HIS67 3.7 13.3 1.0
ZN B:ZN401 4.0 14.8 1.0
C3 B:PFB404 4.1 15.6 1.0
CZ B:PHE140 4.1 16.7 1.0
CE2 B:PHE140 4.3 16.9 1.0
CA B:SER48 4.5 12.6 1.0
CG B:LEU141 4.6 14.6 1.0
F4 B:PFB404 4.7 22.0 1.0
CB B:HIS67 4.7 14.1 1.0
F2 B:PFB404 4.7 18.4 1.0
CD1 B:PHE93 4.8 12.3 1.0
CE1 B:PHE93 4.8 13.6 1.0
C B:SER48 4.8 14.5 1.0
CD1 B:LEU57 4.9 26.1 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: Wed Apr 5 01:27:19 2023

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