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Fluorine in PDB 4dwv: Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol

Enzymatic activity of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol

All present enzymatic activity of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol, PDB code: 4dwv was solved by B.V.Plapp, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.14
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.290, 51.440, 92.490, 91.72, 103.09, 110.11
R / Rfree (%) 12.4 / 14.4

Other elements in 4dwv:

The structure of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol (pdb code 4dwv). 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 Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol, PDB code: 4dwv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 4dwv

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Fluorine binding site 1 out of 10 in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:13.4
occ:1.00
 F2 A:PFB378 0.0 13.4 1.0
C2 A:PFB378 1.3 11.7 1.0
C3 A:PFB378 2.3 12.0 1.0
C1 A:PFB378 2.3 11.3 1.0
F3 A:PFB378 2.7 13.8 1.0
C7N A:NAJ377 2.8 8.6 1.0
C7 A:PFB378 2.9 11.3 1.0
C3N A:NAJ377 3.0 8.2 1.0
O7N A:NAJ377 3.0 9.2 1.0
C2N A:NAJ377 3.4 7.7 1.0
N7N A:NAJ377 3.4 10.0 1.0
C4 A:PFB378 3.6 12.5 1.0
C6 A:PFB378 3.6 12.2 1.0
CD1 A:ILE318 3.7 15.8 1.0
CG2 A:VAL294 3.8 12.9 1.0
C4N A:NAJ377 3.8 10.7 1.0
O1 A:PFB378 3.8 11.4 1.0
C5 A:PFB378 4.0 12.6 1.0
N1N A:NAJ377 4.3 8.5 1.0
CE1 A:PHE93 4.5 10.9 1.0
OG A:SER48 4.5 10.8 1.0
CG2 A:ILE318 4.6 11.8 1.0
CD2 A:LEU116 4.6 18.2 1.0
F4 A:PFB378 4.6 15.6 1.0
C5N A:NAJ377 4.7 10.0 1.0
F6 A:PFB378 4.7 12.9 1.0
CZ A:PHE93 4.7 10.8 1.0
CD2 B:LEU309 4.8 13.9 0.7
CG1 A:ILE318 4.9 11.8 1.0
C6N A:NAJ377 4.9 9.3 1.0

Fluorine binding site 2 out of 10 in 4dwv

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Fluorine binding site 2 out of 10 in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:13.8
occ:1.00
 F3 A:PFB378 0.0 13.8 1.0
C3 A:PFB378 1.3 12.0 1.0
C4 A:PFB378 2.3 12.5 1.0
C2 A:PFB378 2.4 11.7 1.0
F2 A:PFB378 2.7 13.4 1.0
F4 A:PFB378 2.7 15.6 1.0
CG2 A:VAL294 3.4 12.9 1.0
CD1 A:ILE318 3.5 15.8 1.0
C5 A:PFB378 3.6 12.6 1.0
C1 A:PFB378 3.6 11.3 1.0
CD2 B:LEU309 3.7 13.9 0.7
CD2 A:LEU116 3.8 18.2 1.0
C6 A:PFB378 4.1 12.2 1.0
O A:HOH681 4.3 26.7 1.0
CB A:VAL294 4.6 11.7 1.0
CG1 A:VAL294 4.6 14.6 1.0
F5 A:PFB378 4.7 15.0 1.0
CG B:LEU309 4.8 11.1 0.7
CG A:LEU116 4.8 19.7 1.0
CG1 A:ILE318 4.9 11.8 1.0
C7 A:PFB378 4.9 11.3 1.0
CE B:MET306 5.0 20.4 1.0

Fluorine binding site 3 out of 10 in 4dwv

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Fluorine binding site 3 out of 10 in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:15.6
occ:1.00
 F4 A:PFB378 0.0 15.6 1.0
C4 A:PFB378 1.3 12.5 1.0
C5 A:PFB378 2.3 12.6 1.0
C3 A:PFB378 2.3 12.0 1.0
F5 A:PFB378 2.7 15.0 1.0
F3 A:PFB378 2.7 13.8 1.0
CD1 A:LEU57 3.2 16.8 0.4
CD2 A:LEU57 3.3 15.1 0.6
CD2 A:LEU57 3.6 16.4 0.4
C2 A:PFB378 3.6 11.7 1.0
C6 A:PFB378 3.6 12.2 1.0
CD1 A:LEU57 3.7 13.9 0.6
O A:HOH681 3.8 26.7 1.0
CG A:LEU57 4.0 15.4 0.4
O A:HOH682 4.0 38.9 1.0
CD2 A:LEU116 4.0 18.2 1.0
CG A:LEU57 4.1 14.4 0.6
C1 A:PFB378 4.1 11.3 1.0
CG A:LEU116 4.2 19.7 1.0
CB A:LEU116 4.6 16.5 1.0
F2 A:PFB378 4.6 13.4 1.0
F6 A:PFB378 4.7 12.9 1.0
O A:LEU116 4.8 20.6 1.0
CG2 A:VAL294 4.8 12.9 1.0
CG1 A:VAL294 4.8 14.6 1.0
CD2 A:LEU141 4.9 16.9 1.0

Fluorine binding site 4 out of 10 in 4dwv

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Fluorine binding site 4 out of 10 in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:15.0
occ:1.00
 F5 A:PFB378 0.0 15.0 1.0
C5 A:PFB378 1.4 12.6 1.0
C4 A:PFB378 2.3 12.5 1.0
C6 A:PFB378 2.4 12.2 1.0
CD2 A:LEU57 2.7 16.4 0.4
F6 A:PFB378 2.7 12.9 1.0
F4 A:PFB378 2.7 15.6 1.0
CD1 A:LEU57 3.2 13.9 0.6
CZ A:PHE140 3.3 12.3 1.0
CD1 A:LEU141 3.4 13.5 1.0
C3 A:PFB378 3.6 12.0 1.0
C1 A:PFB378 3.6 11.3 1.0
CD2 A:LEU141 3.7 16.9 1.0
CE1 A:PHE140 3.7 12.4 1.0
CG A:LEU57 3.9 15.4 0.4
CG A:LEU141 4.0 12.5 1.0
C2 A:PFB378 4.1 11.7 1.0
CD1 A:LEU57 4.2 16.8 0.4
CE2 A:PHE140 4.3 13.1 1.0
CG A:LEU57 4.3 14.4 0.6
CD2 A:LEU57 4.4 15.1 0.6
CB A:SER48 4.5 11.0 1.0
F3 A:PFB378 4.7 13.8 1.0
C7 A:PFB378 4.9 11.3 1.0
CG A:LEU116 4.9 19.7 1.0
CD1 A:PHE140 5.0 12.4 1.0
CD2 A:LEU116 5.0 18.2 1.0
OG A:SER48 5.0 10.8 1.0

Fluorine binding site 5 out of 10 in 4dwv

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Fluorine binding site 5 out of 10 in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:12.9
occ:1.00
 F6 A:PFB378 0.0 12.9 1.0
C6 A:PFB378 1.3 12.2 1.0
C5 A:PFB378 2.3 12.6 1.0
C1 A:PFB378 2.4 11.3 1.0
F5 A:PFB378 2.7 15.0 1.0
C7 A:PFB378 2.8 11.3 1.0
O1 A:PFB378 3.1 11.4 1.0
CD1 A:LEU141 3.2 13.5 1.0
CB A:SER48 3.2 11.0 1.0
NE2 A:HIS67 3.3 11.0 1.0
CE1 A:HIS67 3.4 10.3 1.0
CD2 A:HIS67 3.5 10.1 1.0
C4 A:PFB378 3.6 12.5 1.0
C2 A:PFB378 3.6 11.7 1.0
OG A:SER48 3.7 10.8 1.0
ND1 A:HIS67 3.7 11.0 1.0
CG A:HIS67 3.8 10.0 1.0
CZ A:PHE140 4.0 12.3 1.0
C3 A:PFB378 4.1 12.0 1.0
ZN A:ZN375 4.1 11.2 1.0
CE2 A:PHE140 4.3 13.1 1.0
CG A:LEU141 4.6 12.5 1.0
CA A:SER48 4.6 10.5 1.0
F4 A:PFB378 4.7 15.6 1.0
F2 A:PFB378 4.7 13.4 1.0
CB A:HIS67 4.7 10.6 1.0
CD2 A:LEU57 4.7 16.4 0.4
CD1 A:LEU57 4.8 13.9 0.6
CD1 A:PHE93 4.8 10.3 1.0
C A:SER48 4.8 11.1 1.0
CE1 A:PHE93 4.8 10.9 1.0

Fluorine binding site 6 out of 10 in 4dwv

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Fluorine binding site 6 out of 10 in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:16.5
occ:1.00
 F2 B:PFB378 0.0 16.5 1.0
C2 B:PFB378 1.3 15.3 1.0
C3 B:PFB378 2.3 15.0 1.0
C1 B:PFB378 2.4 14.4 1.0
F3 B:PFB378 2.7 17.0 1.0
C7 B:PFB378 2.9 14.1 1.0
C7N B:NAJ377 2.9 11.7 1.0
O7N B:NAJ377 3.0 12.6 1.0
C3N B:NAJ377 3.1 11.9 1.0
C2N B:NAJ377 3.4 11.3 1.0
N7N B:NAJ377 3.5 12.0 1.0
C4 B:PFB378 3.6 16.4 1.0
C6 B:PFB378 3.6 14.7 1.0
CD1 B:ILE318 3.7 19.7 1.0
O1 B:PFB378 3.7 14.5 1.0
CG2 B:VAL294 3.8 16.0 1.0
C4N B:NAJ377 3.8 13.2 1.0
C5 B:PFB378 4.1 15.4 1.0
N1N B:NAJ377 4.3 11.3 1.0
OG B:SER48 4.5 13.5 1.0
CE1 B:PHE93 4.5 13.6 1.0
CG2 B:ILE318 4.6 15.4 1.0
CD2 B:LEU116 4.6 23.4 1.0
F4 B:PFB378 4.7 18.5 1.0
F6 B:PFB378 4.7 15.8 1.0
CZ B:PHE93 4.7 14.0 1.0
C5N B:NAJ377 4.7 12.2 1.0
CD2 A:LEU309 4.7 16.6 0.7
C6N B:NAJ377 4.9 12.7 1.0
CG1 B:ILE318 4.9 14.5 1.0

Fluorine binding site 7 out of 10 in 4dwv

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Fluorine binding site 7 out of 10 in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:17.0
occ:1.00
 F3 B:PFB378 0.0 17.0 1.0
C3 B:PFB378 1.3 15.0 1.0
C2 B:PFB378 2.3 15.3 1.0
C4 B:PFB378 2.4 16.4 1.0
F2 B:PFB378 2.7 16.5 1.0
F4 B:PFB378 2.7 18.5 1.0
CG2 B:VAL294 3.4 16.0 1.0
C5 B:PFB378 3.6 15.4 1.0
CD1 B:ILE318 3.6 19.7 1.0
CD2 A:LEU309 3.6 16.6 0.7
C1 B:PFB378 3.6 14.4 1.0
CD2 B:LEU116 3.7 23.4 1.0
O A:HOH981 4.0 48.1 1.0
C6 B:PFB378 4.1 14.7 1.0
CG1 B:VAL294 4.6 17.6 1.0
CB B:VAL294 4.6 14.4 1.0
F5 B:PFB378 4.7 18.2 1.0
CG A:LEU309 4.8 14.1 0.7
CG B:LEU116 4.8 24.4 1.0
C7 B:PFB378 4.9 14.1 1.0
CG1 B:ILE318 4.9 14.5 1.0

Fluorine binding site 8 out of 10 in 4dwv

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Fluorine binding site 8 out of 10 in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:18.5
occ:1.00
 F4 B:PFB378 0.0 18.5 1.0
C4 B:PFB378 1.3 16.4 1.0
C3 B:PFB378 2.3 15.0 1.0
C5 B:PFB378 2.4 15.4 1.0
F3 B:PFB378 2.7 17.0 1.0
F5 B:PFB378 2.7 18.2 1.0
CD2 B:LEU57 3.3 22.1 1.0
C2 B:PFB378 3.6 15.3 1.0
C6 B:PFB378 3.6 14.7 1.0
CD1 B:LEU57 3.6 25.0 1.0
O B:HOH776 3.6 41.2 1.0
O A:HOH981 3.8 48.1 1.0
O B:HOH915 3.8 50.9 1.0
CD2 B:LEU116 3.9 23.4 1.0
CG B:LEU57 4.0 22.9 1.0
C1 B:PFB378 4.1 14.4 1.0
CG B:LEU116 4.2 24.4 1.0
F2 B:PFB378 4.7 16.5 1.0
F6 B:PFB378 4.7 15.8 1.0
CB B:LEU116 4.7 21.9 1.0
CG2 B:VAL294 4.8 16.0 1.0
CG1 B:VAL294 4.9 17.6 1.0
CD2 B:LEU141 5.0 20.7 1.0

Fluorine binding site 9 out of 10 in 4dwv

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Fluorine binding site 9 out of 10 in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:18.2
occ:1.00
 F5 B:PFB378 0.0 18.2 1.0
C5 B:PFB378 1.3 15.4 1.0
C6 B:PFB378 2.3 14.7 1.0
C4 B:PFB378 2.4 16.4 1.0
F6 B:PFB378 2.7 15.8 1.0
F4 B:PFB378 2.7 18.5 1.0
CD1 B:LEU57 3.1 25.0 1.0
CZ B:PHE140 3.3 17.5 1.0
CD1 B:LEU141 3.4 17.5 1.0
C3 B:PFB378 3.6 15.0 1.0
C1 B:PFB378 3.6 14.4 1.0
CE1 B:PHE140 3.8 16.5 1.0
CD2 B:LEU141 3.8 20.7 1.0
CG B:LEU141 4.0 16.1 1.0
C2 B:PFB378 4.1 15.3 1.0
CE2 B:PHE140 4.2 17.2 1.0
CG B:LEU57 4.4 22.9 1.0
O B:HOH776 4.4 41.2 1.0
CB B:SER48 4.4 12.8 1.0
CD2 B:LEU57 4.5 22.1 1.0
F3 B:PFB378 4.7 17.0 1.0
O B:HOH755 4.7 35.6 1.0
C7 B:PFB378 4.9 14.1 1.0
CG B:LEU116 4.9 24.4 1.0
CD2 B:LEU116 5.0 23.4 1.0
O B:SER48 5.0 15.1 1.0
CD1 B:PHE140 5.0 16.0 1.0

Fluorine binding site 10 out of 10 in 4dwv

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Fluorine binding site 10 out of 10 in the Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Horse Alcohol Dehydrogenase Complexed with Nad+ and 2,3,4,5,6- Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:15.8
occ:1.00
 F6 B:PFB378 0.0 15.8 1.0
C6 B:PFB378 1.3 14.7 1.0
C5 B:PFB378 2.3 15.4 1.0
C1 B:PFB378 2.3 14.4 1.0
F5 B:PFB378 2.7 18.2 1.0
C7 B:PFB378 2.8 14.1 1.0
O1 B:PFB378 3.1 14.5 1.0
CD1 B:LEU141 3.2 17.5 1.0
CB B:SER48 3.2 12.8 1.0
NE2 B:HIS67 3.3 14.7 1.0
CE1 B:HIS67 3.4 13.9 1.0
CD2 B:HIS67 3.5 12.6 1.0
C4 B:PFB378 3.6 16.4 1.0
C2 B:PFB378 3.6 15.3 1.0
ND1 B:HIS67 3.7 13.6 1.0
CG B:HIS67 3.7 12.8 1.0
OG B:SER48 3.7 13.5 1.0
ZN B:ZN375 4.1 14.3 1.0
C3 B:PFB378 4.1 15.0 1.0
CZ B:PHE140 4.1 17.5 1.0
CE2 B:PHE140 4.3 17.2 1.0
CG B:LEU141 4.6 16.1 1.0
CA B:SER48 4.6 13.3 1.0
F4 B:PFB378 4.7 18.5 1.0
F2 B:PFB378 4.7 16.5 1.0
CB B:HIS67 4.7 13.1 1.0
CD1 B:PHE93 4.8 13.3 1.0
C B:SER48 4.8 14.4 1.0
CE1 B:PHE93 4.8 13.6 1.0
CD1 B:LEU57 4.9 25.0 1.0

Reference:

B.V.Plapp, S.Ramaswamy. Atomic-Resolution Structures of Horse Liver Alcohol Dehydrogenase with Nad(+) and Fluoroalcohols Define Strained Michaelis Complexes. Biochemistry V. 51 4035 2012.
ISSN: ISSN 0006-2960
PubMed: 22531044
DOI: 10.1021/BI300378N
Page generated: Sun Dec 13 12:01:43 2020

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