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Fluorine in PDB 4ng5: V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol

Enzymatic activity of V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol

All present enzymatic activity of V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol, PDB code: 4ng5 was solved by B.V.Plapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.91 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.520, 51.560, 92.550, 91.80, 103.05, 110.30
R / Rfree (%) 12 / 13.7

Other elements in 4ng5:

The structure of V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol (pdb code 4ng5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol, PDB code: 4ng5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 4ng5

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Fluorine binding site 1 out of 10 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E 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:16.4
occ:0.75
 F2 A:PFB378 0.0 16.4 0.8
C2 A:PFB378 1.3 13.7 0.8
C3 A:PFB378 2.3 13.9 0.8
C1 A:PFB378 2.4 13.8 0.8
F3 A:PFB378 2.7 15.8 0.8
C7N A:NAJ377 2.8 10.7 1.0
C7 A:PFB378 2.9 14.5 0.8
O7N A:NAJ377 3.0 11.4 1.0
C3N A:NAJ377 3.0 11.0 1.0
N7N A:NAJ377 3.3 10.7 1.0
C2N A:NAJ377 3.4 9.9 1.0
C4 A:PFB378 3.5 15.4 0.8
C6 A:PFB378 3.6 14.9 0.8
CG2 A:VAL294 3.7 13.9 1.0
CD1 A:ILE318 3.8 16.7 1.0
O1 A:PFB378 3.8 14.2 0.8
C4N A:NAJ377 3.9 13.3 1.0
C5 A:PFB378 4.1 15.0 0.8
N1N A:NAJ377 4.4 10.4 1.0
CE1 A:PHE93 4.6 11.9 1.0
CG2 A:ILE318 4.6 12.3 1.0
F4 A:PFB378 4.6 19.0 0.8
OG A:SER48 4.6 13.8 1.0
CD2 A:LEU116 4.7 20.5 1.0
CD2 B:LEU309 4.7 14.2 0.7
F6 A:PFB378 4.7 16.0 0.8
CZ A:PHE93 4.8 12.6 1.0
C5N A:NAJ377 4.9 11.8 1.0
CG1 A:ILE318 5.0 13.4 1.0

Fluorine binding site 2 out of 10 in 4ng5

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Fluorine binding site 2 out of 10 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E 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:15.8
occ:0.75
 F3 A:PFB378 0.0 15.8 0.8
C3 A:PFB378 1.3 13.9 0.8
C4 A:PFB378 2.3 15.4 0.8
C2 A:PFB378 2.4 13.7 0.8
F4 A:PFB378 2.7 19.0 0.8
F2 A:PFB378 2.7 16.4 0.8
CG2 A:VAL294 3.5 13.9 1.0
C5 A:PFB378 3.6 15.0 0.8
CD1 A:ILE318 3.6 16.7 1.0
C1 A:PFB378 3.6 13.8 0.8
CD2 B:LEU309 3.7 14.2 0.7
CD2 A:LEU116 3.9 20.5 1.0
C6 A:PFB378 4.1 14.9 0.8
O A:HOH681 4.2 24.3 1.0
CG1 A:VAL294 4.6 14.2 1.0
CB A:VAL294 4.6 12.7 1.0
F5 A:PFB378 4.7 17.4 0.8
CG B:LEU309 4.8 12.2 0.7
CG A:LEU116 4.9 19.6 1.0
CE B:MET306 4.9 19.2 1.0
C7 A:PFB378 4.9 14.5 0.8
CG1 A:ILE318 5.0 13.4 1.0

Fluorine binding site 3 out of 10 in 4ng5

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Fluorine binding site 3 out of 10 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E 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:19.0
occ:0.75
 F4 A:PFB378 0.0 19.0 0.8
C4 A:PFB378 1.3 15.4 0.8
C3 A:PFB378 2.3 13.9 0.8
C5 A:PFB378 2.3 15.0 0.8
F3 A:PFB378 2.7 15.8 0.8
F5 A:PFB378 2.7 17.4 0.8
CD1 A:LEU57 3.2 14.8 0.4
CD2 A:LEU57 3.3 14.5 0.6
CD2 A:LEU57 3.5 16.1 0.4
C2 A:PFB378 3.6 13.7 0.8
C6 A:PFB378 3.6 14.9 0.8
CD1 A:LEU57 3.8 15.4 0.6
O A:HOH681 3.8 24.3 1.0
CG A:LEU57 4.0 14.5 0.4
CD2 A:LEU116 4.1 20.5 1.0
C1 A:PFB378 4.1 13.8 0.8
CG A:LEU116 4.1 19.6 1.0
CG A:LEU57 4.2 15.4 0.6
O A:HOH682 4.2 32.2 1.0
CB A:LEU116 4.6 16.6 1.0
F2 A:PFB378 4.6 16.4 0.8
F6 A:PFB378 4.7 16.0 0.8
O A:LEU116 4.8 21.1 1.0
CG2 A:VAL294 4.8 13.9 1.0
CG1 A:VAL294 4.9 14.2 1.0
CD2 A:LEU141 4.9 16.6 1.0

Fluorine binding site 4 out of 10 in 4ng5

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Fluorine binding site 4 out of 10 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E 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:17.4
occ:0.75
 F5 A:PFB378 0.0 17.4 0.8
C5 A:PFB378 1.4 15.0 0.8
C4 A:PFB378 2.4 15.4 0.8
C6 A:PFB378 2.4 14.9 0.8
F4 A:PFB378 2.7 19.0 0.8
F6 A:PFB378 2.7 16.0 0.8
CD2 A:LEU57 2.7 16.1 0.4
CD1 A:LEU57 3.2 15.4 0.6
CD1 A:LEU141 3.3 13.9 1.0
CZ A:PHE140 3.3 14.1 1.0
C3 A:PFB378 3.6 13.9 0.8
CD2 A:LEU141 3.6 16.6 1.0
C1 A:PFB378 3.6 13.8 0.8
CE1 A:PHE140 3.8 14.0 1.0
CG A:LEU141 3.9 14.3 1.0
CG A:LEU57 4.0 14.5 0.4
C2 A:PFB378 4.1 13.7 0.8
CD1 A:LEU57 4.2 14.8 0.4
CE2 A:PHE140 4.3 14.8 1.0
CG A:LEU57 4.4 15.4 0.6
CD2 A:LEU57 4.4 14.5 0.6
CB A:SER48 4.5 12.7 1.0
F3 A:PFB378 4.7 15.8 0.8
CG A:LEU116 4.8 19.6 1.0
C7 A:PFB378 4.9 14.5 0.8
CD1 A:PHE140 5.0 12.5 1.0
CD2 A:LEU116 5.0 20.5 1.0

Fluorine binding site 5 out of 10 in 4ng5

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Fluorine binding site 5 out of 10 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E 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:16.0
occ:0.75
 F6 A:PFB378 0.0 16.0 0.8
C6 A:PFB378 1.3 14.9 0.8
C5 A:PFB378 2.3 15.0 0.8
C1 A:PFB378 2.4 13.8 0.8
F5 A:PFB378 2.7 17.4 0.8
C7 A:PFB378 2.8 14.5 0.8
O1 A:PFB378 3.1 14.2 0.8
CD1 A:LEU141 3.2 13.9 1.0
NE2 A:HIS67 3.2 15.8 1.0
CB A:SER48 3.3 12.7 1.0
CE1 A:HIS67 3.4 14.1 1.0
CD2 A:HIS67 3.4 13.8 1.0
C4 A:PFB378 3.6 15.4 0.8
C2 A:PFB378 3.6 13.7 0.8
OG A:SER48 3.7 13.8 1.0
ND1 A:HIS67 3.8 12.6 1.0
CG A:HIS67 3.8 12.1 1.0
ZN A:ZN375 4.0 11.9 0.6
C3 A:PFB378 4.1 13.9 0.8
CZ A:PHE140 4.1 14.1 1.0
CE2 A:PHE140 4.3 14.8 1.0
CG A:LEU141 4.5 14.3 1.0
CA A:SER48 4.6 11.9 1.0
CD1 A:PHE93 4.7 11.0 1.0
F4 A:PFB378 4.7 19.0 0.8
F2 A:PFB378 4.7 16.4 0.8
CE1 A:PHE93 4.7 11.9 1.0
CB A:HIS67 4.7 11.5 1.0
CD2 A:LEU57 4.8 16.1 0.4
CD1 A:LEU57 4.8 15.4 0.6
C A:SER48 4.9 12.1 1.0
CG A:PHE93 5.0 10.7 1.0

Fluorine binding site 6 out of 10 in 4ng5

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Fluorine binding site 6 out of 10 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E 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:18.0
occ:0.75
 F2 B:PFB378 0.0 18.0 0.8
C2 B:PFB378 1.3 16.2 0.8
C3 B:PFB378 2.3 15.5 0.8
C1 B:PFB378 2.4 15.5 0.8
F3 B:PFB378 2.7 17.3 0.8
C7N B:NAJ377 2.9 12.1 1.0
C7 B:PFB378 3.0 15.0 0.8
O7N B:NAJ377 3.0 13.2 1.0
C3N B:NAJ377 3.1 12.2 1.0
N7N B:NAJ377 3.4 12.5 1.0
C2N B:NAJ377 3.4 11.9 1.0
C4 B:PFB378 3.6 18.0 0.8
C6 B:PFB378 3.6 15.9 0.8
CG2 B:VAL294 3.7 16.5 1.0
CD1 B:ILE318 3.8 19.3 1.0
O1 B:PFB378 3.8 16.4 0.8
C4N B:NAJ377 3.9 15.6 1.0
C5 B:PFB378 4.1 16.5 0.8
N1N B:NAJ377 4.4 12.7 1.0
OG B:SER48 4.6 15.3 1.0
F4 B:PFB378 4.6 20.6 0.8
CD2 B:LEU116 4.6 24.3 1.0
CE1 B:PHE93 4.7 14.1 1.0
CG2 B:ILE318 4.7 13.8 1.0
CD2 A:LEU309 4.7 16.3 0.7
F6 B:PFB378 4.7 17.5 0.8
CZ B:PHE93 4.9 14.6 1.0
C5N B:NAJ377 4.9 14.0 1.0

Fluorine binding site 7 out of 10 in 4ng5

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Fluorine binding site 7 out of 10 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E 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:17.3
occ:0.75
 F3 B:PFB378 0.0 17.3 0.8
C3 B:PFB378 1.4 15.5 0.8
C4 B:PFB378 2.4 18.0 0.8
C2 B:PFB378 2.4 16.2 0.8
F4 B:PFB378 2.7 20.6 0.8
F2 B:PFB378 2.7 18.0 0.8
CG2 B:VAL294 3.5 16.5 1.0
C5 B:PFB378 3.6 16.5 0.8
C1 B:PFB378 3.7 15.5 0.8
CD2 A:LEU309 3.7 16.3 0.7
CD1 B:ILE318 3.8 19.3 1.0
CD2 B:LEU116 3.8 24.3 1.0
C6 B:PFB378 4.1 15.9 0.8
O B:HOH934 4.2 37.2 1.0
CG1 B:VAL294 4.5 17.0 1.0
CB B:VAL294 4.6 14.6 1.0
F5 B:PFB378 4.7 18.9 0.8
CG A:LEU309 4.8 13.9 0.7
CG B:LEU116 4.9 24.4 1.0
C7 B:PFB378 4.9 15.0 0.8

Fluorine binding site 8 out of 10 in 4ng5

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Fluorine binding site 8 out of 10 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E 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:20.6
occ:0.75
 F4 B:PFB378 0.0 20.6 0.8
C4 B:PFB378 1.3 18.0 0.8
C3 B:PFB378 2.3 15.5 0.8
C5 B:PFB378 2.4 16.5 0.8
F3 B:PFB378 2.7 17.3 0.8
F5 B:PFB378 2.7 18.9 0.8
CD2 B:LEU57 3.3 20.1 1.0
C2 B:PFB378 3.6 16.2 0.8
C6 B:PFB378 3.6 15.9 0.8
CD1 B:LEU57 3.6 24.7 1.0
O B:HOH934 3.8 37.2 1.0
O B:HOH776 3.8 44.6 1.0
CD2 B:LEU116 3.9 24.3 1.0
CG B:LEU57 4.1 22.5 1.0
C1 B:PFB378 4.1 15.5 0.8
CG B:LEU116 4.2 24.4 1.0
F2 B:PFB378 4.6 18.0 0.8
F6 B:PFB378 4.7 17.5 0.8
CB B:LEU116 4.7 19.5 1.0
CG1 B:VAL294 4.9 17.0 1.0
CG2 B:VAL294 4.9 16.5 1.0

Fluorine binding site 9 out of 10 in 4ng5

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Fluorine binding site 9 out of 10 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E 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:18.9
occ:0.75
 F5 B:PFB378 0.0 18.9 0.8
C5 B:PFB378 1.3 16.5 0.8
C4 B:PFB378 2.3 18.0 0.8
C6 B:PFB378 2.4 15.9 0.8
F4 B:PFB378 2.7 20.6 0.8
F6 B:PFB378 2.7 17.5 0.8
CD1 B:LEU57 3.1 24.7 1.0
CZ B:PHE140 3.3 16.9 1.0
CD1 B:LEU141 3.4 17.0 1.0
C3 B:PFB378 3.6 15.5 0.8
C1 B:PFB378 3.6 15.5 0.8
CE1 B:PHE140 3.8 15.5 1.0
CD2 B:LEU141 3.8 18.9 1.0
CG B:LEU141 4.0 16.4 1.0
C2 B:PFB378 4.1 16.2 0.8
CE2 B:PHE140 4.3 17.5 1.0
CG B:LEU57 4.4 22.5 1.0
O B:HOH776 4.4 44.6 1.0
CB B:SER48 4.5 14.8 1.0
CD2 B:LEU57 4.5 20.1 1.0
F3 B:PFB378 4.7 17.3 0.8
O B:HOH755 4.8 42.8 1.0
CG B:LEU116 4.8 24.4 1.0
C7 B:PFB378 4.9 15.0 0.8
CD2 B:LEU116 4.9 24.3 1.0

Fluorine binding site 10 out of 10 in 4ng5

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Fluorine binding site 10 out of 10 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E 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:17.5
occ:0.75
 F6 B:PFB378 0.0 17.5 0.8
C6 B:PFB378 1.3 15.9 0.8
C5 B:PFB378 2.3 16.5 0.8
C1 B:PFB378 2.4 15.5 0.8
F5 B:PFB378 2.7 18.9 0.8
C7 B:PFB378 2.8 15.0 0.8
O1 B:PFB378 3.1 16.4 0.8
CD1 B:LEU141 3.2 17.0 1.0
NE2 B:HIS67 3.2 16.7 1.0
CB B:SER48 3.3 14.8 1.0
CE1 B:HIS67 3.4 15.8 1.0
CD2 B:HIS67 3.4 15.6 1.0
C4 B:PFB378 3.6 18.0 0.8
C2 B:PFB378 3.6 16.2 0.8
OG B:SER48 3.7 15.3 1.0
ND1 B:HIS67 3.8 14.3 1.0
CG B:HIS67 3.8 13.5 1.0
ZN B:ZN375 4.0 13.7 0.6
C3 B:PFB378 4.1 15.5 0.8
CZ B:PHE140 4.2 16.9 1.0
CE2 B:PHE140 4.3 17.5 1.0
CG B:LEU141 4.6 16.4 1.0
CA B:SER48 4.6 15.0 1.0
F4 B:PFB378 4.7 20.6 0.8
CD1 B:PHE93 4.7 12.4 1.0
CE1 B:PHE93 4.7 14.1 1.0
F2 B:PFB378 4.7 18.0 0.8
CB B:HIS67 4.8 13.5 1.0
C B:SER48 4.8 15.1 1.0
CD1 B:LEU57 4.9 24.7 1.0

Reference:

A.Yahashiri, J.K.Rubach, B.V.Plapp. Effects of Cavities at the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase on Structure, Dynamics and Catalysis. Biochemistry V. 53 881 2014.
ISSN: ISSN 0006-2960
PubMed: 24437493
DOI: 10.1021/BI401583F
Page generated: Thu Aug 1 04:15:37 2024

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