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Fluorine in PDB 4nfh: V207A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,3, 4,5,6-Pentafluorobenzyl Alcohol

Enzymatic activity of V207A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,3, 4,5,6-Pentafluorobenzyl Alcohol

All present enzymatic activity of V207A 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 V207A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,3, 4,5,6-Pentafluorobenzyl Alcohol, PDB code: 4nfh 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) 19.84 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.490, 51.230, 92.320, 91.96, 103.00, 110.28
R / Rfree (%) 13.5 / 16.6

Other elements in 4nfh:

The structure of V207A 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 V207A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,3, 4,5,6-Pentafluorobenzyl Alcohol (pdb code 4nfh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the V207A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,3, 4,5,6-Pentafluorobenzyl Alcohol, PDB code: 4nfh:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 4nfh

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Fluorine binding site 1 out of 10 in the V207A 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 V207A 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:13.8
occ:1.00
 F2 A:PFB378 0.0 13.8 1.0
C2 A:PFB378 1.3 12.9 1.0
C3 A:PFB378 2.3 13.2 1.0
C1 A:PFB378 2.4 11.4 1.0
F3 A:PFB378 2.7 14.7 1.0
C7N A:NAJ377 2.8 9.4 1.0
C7 A:PFB378 2.9 12.1 1.0
C3N A:NAJ377 3.0 9.3 1.0
O7N A:NAJ377 3.0 9.6 1.0
C2N A:NAJ377 3.4 9.2 1.0
N7N A:NAJ377 3.4 10.2 1.0
C4 A:PFB378 3.6 13.2 1.0
C6 A:PFB378 3.6 12.6 1.0
CD1 A:ILE318 3.7 14.4 1.0
C4N A:NAJ377 3.7 10.9 1.0
O1 A:PFB378 3.8 11.2 1.0
CG2 A:VAL294 3.8 14.2 1.0
C5 A:PFB378 4.1 13.6 1.0
N1N A:NAJ377 4.3 8.9 1.0
CE1 A:PHE93 4.5 10.9 1.0
OG A:SER48 4.5 10.6 1.0
CG2 A:ILE318 4.5 12.2 1.0
CD2 A:LEU116 4.6 19.2 1.0
F4 A:PFB378 4.6 16.0 1.0
C5N A:NAJ377 4.7 9.8 1.0
F6 A:PFB378 4.7 13.5 1.0
CZ A:PHE93 4.7 11.4 1.0
CD2 B:LEU309 4.8 14.1 0.7
C6N A:NAJ377 4.9 8.9 1.0
CG1 A:ILE318 5.0 10.7 1.0

Fluorine binding site 2 out of 10 in 4nfh

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Fluorine binding site 2 out of 10 in the V207A 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 V207A 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:14.7
occ:1.00
 F3 A:PFB378 0.0 14.7 1.0
C3 A:PFB378 1.3 13.2 1.0
C4 A:PFB378 2.3 13.2 1.0
C2 A:PFB378 2.4 12.9 1.0
F4 A:PFB378 2.7 16.0 1.0
F2 A:PFB378 2.7 13.8 1.0
CG2 A:VAL294 3.5 14.2 1.0
CD1 A:ILE318 3.6 14.4 1.0
C5 A:PFB378 3.6 13.6 1.0
C1 A:PFB378 3.7 11.4 1.0
CD2 B:LEU309 3.7 14.1 0.7
CD2 A:LEU116 3.7 19.2 1.0
C6 A:PFB378 4.1 12.6 1.0
O A:HOH681 4.1 33.7 1.0
CB A:VAL294 4.7 11.7 1.0
CG1 A:VAL294 4.7 14.1 1.0
F5 A:PFB378 4.7 15.4 1.0
CG A:LEU116 4.8 19.1 1.0
CG B:LEU309 4.8 12.5 0.7
CE B:MET306 4.9 22.1 1.0
CG1 A:ILE318 4.9 10.7 1.0
C7 A:PFB378 4.9 12.1 1.0

Fluorine binding site 3 out of 10 in 4nfh

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Fluorine binding site 3 out of 10 in the V207A 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 V207A 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:1.00
 F4 A:PFB378 0.0 16.0 1.0
C4 A:PFB378 1.3 13.2 1.0
C5 A:PFB378 2.3 13.6 1.0
C3 A:PFB378 2.3 13.2 1.0
F3 A:PFB378 2.7 14.7 1.0
F5 A:PFB378 2.7 15.4 1.0
CD1 A:LEU57 3.2 17.8 0.3
CD2 A:LEU57 3.3 15.6 0.7
C6 A:PFB378 3.6 12.6 1.0
C2 A:PFB378 3.6 12.9 1.0
CD1 A:LEU57 3.6 12.7 0.7
O A:HOH681 3.7 33.7 1.0
CD2 A:LEU57 3.8 18.2 0.3
O A:HOH682 3.9 44.8 1.0
CD2 A:LEU116 3.9 19.2 1.0
CG A:LEU57 4.1 13.4 0.7
C1 A:PFB378 4.1 11.4 1.0
CG A:LEU57 4.1 16.1 0.3
CG A:LEU116 4.2 19.1 1.0
F2 A:PFB378 4.6 13.8 1.0
CB A:LEU116 4.6 17.8 1.0
F6 A:PFB378 4.7 13.5 1.0
O A:LEU116 4.8 21.8 1.0
CG2 A:VAL294 4.8 14.2 1.0
CG1 A:VAL294 4.9 14.1 1.0
CD2 A:LEU141 4.9 15.3 1.0

Fluorine binding site 4 out of 10 in 4nfh

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Fluorine binding site 4 out of 10 in the V207A 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 V207A 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:15.4
occ:1.00
 F5 A:PFB378 0.0 15.4 1.0
C5 A:PFB378 1.4 13.6 1.0
C6 A:PFB378 2.4 12.6 1.0
C4 A:PFB378 2.4 13.2 1.0
F6 A:PFB378 2.7 13.5 1.0
F4 A:PFB378 2.7 16.0 1.0
CD2 A:LEU57 2.8 18.2 0.3
CD1 A:LEU57 3.1 12.7 0.7
CZ A:PHE140 3.3 12.7 1.0
CD1 A:LEU141 3.4 13.3 1.0
C3 A:PFB378 3.6 13.2 1.0
C1 A:PFB378 3.7 11.4 1.0
CD2 A:LEU141 3.7 15.3 1.0
CE1 A:PHE140 3.7 12.7 1.0
CG A:LEU141 3.9 13.1 1.0
CG A:LEU57 4.0 16.1 0.3
CD1 A:LEU57 4.1 17.8 0.3
C2 A:PFB378 4.1 12.9 1.0
CE2 A:PHE140 4.3 12.8 1.0
CG A:LEU57 4.3 13.4 0.7
CD2 A:LEU57 4.5 15.6 0.7
CB A:SER48 4.5 10.5 1.0
O A:HOH1046 4.7 42.6 1.0
F3 A:PFB378 4.7 14.7 1.0
C7 A:PFB378 4.9 12.1 1.0
CD1 A:PHE140 4.9 12.3 1.0
CG A:LEU116 4.9 19.1 1.0
CD2 A:LEU116 5.0 19.2 1.0
OG A:SER48 5.0 10.6 1.0

Fluorine binding site 5 out of 10 in 4nfh

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Fluorine binding site 5 out of 10 in the V207A 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 V207A 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:13.5
occ:1.00
 F6 A:PFB378 0.0 13.5 1.0
C6 A:PFB378 1.3 12.6 1.0
C1 A:PFB378 2.3 11.4 1.0
C5 A:PFB378 2.4 13.6 1.0
F5 A:PFB378 2.7 15.4 1.0
C7 A:PFB378 2.8 12.1 1.0
O1 A:PFB378 3.2 11.2 1.0
CB A:SER48 3.2 10.5 1.0
CD1 A:LEU141 3.2 13.3 1.0
NE2 A:HIS67 3.3 11.3 1.0
CE1 A:HIS67 3.4 10.1 1.0
CD2 A:HIS67 3.5 11.2 1.0
C2 A:PFB378 3.6 12.9 1.0
C4 A:PFB378 3.6 13.2 1.0
ND1 A:HIS67 3.7 9.9 1.0
OG A:SER48 3.7 10.6 1.0
CG A:HIS67 3.7 9.6 1.0
CZ A:PHE140 4.0 12.7 1.0
C3 A:PFB378 4.1 13.2 1.0
ZN A:ZN375 4.1 11.7 1.0
CE2 A:PHE140 4.3 12.8 1.0
CG A:LEU141 4.5 13.1 1.0
CA A:SER48 4.6 11.3 1.0
F4 A:PFB378 4.7 16.0 1.0
CB A:HIS67 4.7 10.2 1.0
F2 A:PFB378 4.7 13.8 1.0
CD1 A:PHE93 4.7 9.7 1.0
CD1 A:LEU57 4.8 12.7 0.7
C A:SER48 4.8 11.6 1.0
CE1 A:PHE93 4.8 10.9 1.0

Fluorine binding site 6 out of 10 in 4nfh

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Fluorine binding site 6 out of 10 in the V207A 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 V207A 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:14.8
occ:1.00
 F2 B:PFB378 0.0 14.8 1.0
C2 B:PFB378 1.3 14.8 1.0
C3 B:PFB378 2.3 14.7 1.0
C1 B:PFB378 2.4 12.8 1.0
F3 B:PFB378 2.7 15.5 1.0
C7N B:NAJ377 2.9 11.2 1.0
C7 B:PFB378 2.9 12.8 1.0
O7N B:NAJ377 3.0 10.9 1.0
C3N B:NAJ377 3.0 10.7 1.0
C2N B:NAJ377 3.3 10.3 1.0
N7N B:NAJ377 3.4 10.8 1.0
C4 B:PFB378 3.6 14.3 1.0
C6 B:PFB378 3.6 12.8 1.0
CD1 B:ILE318 3.7 17.3 1.0
O1 B:PFB378 3.8 12.3 1.0
CG2 B:VAL294 3.8 16.5 1.0
C4N B:NAJ377 3.8 13.9 1.0
C5 B:PFB378 4.1 15.0 1.0
N1N B:NAJ377 4.3 10.5 1.0
OG B:SER48 4.5 11.2 1.0
CE1 B:PHE93 4.5 11.8 1.0
CG2 B:ILE318 4.6 11.9 1.0
CD2 B:LEU116 4.6 19.7 1.0
F4 B:PFB378 4.7 16.6 1.0
C5N B:NAJ377 4.7 10.6 1.0
F6 B:PFB378 4.7 14.5 1.0
CZ B:PHE93 4.7 12.5 1.0
CD2 A:LEU309 4.8 14.7 0.7
CG1 B:ILE318 4.9 12.2 1.0
C6N B:NAJ377 4.9 11.2 1.0

Fluorine binding site 7 out of 10 in 4nfh

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Fluorine binding site 7 out of 10 in the V207A 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 V207A 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:15.5
occ:1.00
 F3 B:PFB378 0.0 15.5 1.0
C3 B:PFB378 1.3 14.7 1.0
C4 B:PFB378 2.3 14.3 1.0
C2 B:PFB378 2.4 14.8 1.0
F2 B:PFB378 2.7 14.8 1.0
F4 B:PFB378 2.7 16.6 1.0
CG2 B:VAL294 3.5 16.5 1.0
C5 B:PFB378 3.6 15.0 1.0
CD1 B:ILE318 3.6 17.3 1.0
C1 B:PFB378 3.7 12.8 1.0
CD2 A:LEU309 3.7 14.7 0.7
CD2 B:LEU116 3.8 19.7 1.0
C6 B:PFB378 4.1 12.8 1.0
CG1 B:VAL294 4.5 16.0 1.0
CB B:VAL294 4.7 13.7 1.0
F5 B:PFB378 4.7 16.8 1.0
CG B:LEU116 4.8 21.4 1.0
CG A:LEU309 4.8 13.0 0.7
C7 B:PFB378 4.9 12.8 1.0
CG1 B:ILE318 5.0 12.2 1.0

Fluorine binding site 8 out of 10 in 4nfh

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Fluorine binding site 8 out of 10 in the V207A 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 V207A 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:16.6
occ:1.00
 F4 B:PFB378 0.0 16.6 1.0
C4 B:PFB378 1.3 14.3 1.0
C3 B:PFB378 2.3 14.7 1.0
C5 B:PFB378 2.4 15.0 1.0
F3 B:PFB378 2.7 15.5 1.0
F5 B:PFB378 2.7 16.8 1.0
CD2 B:LEU57 3.3 19.6 1.0
CD1 B:LEU57 3.6 20.3 1.0
C2 B:PFB378 3.6 14.8 1.0
C6 B:PFB378 3.6 12.8 1.0
O B:HOH776 3.7 43.5 1.0
CD2 B:LEU116 4.0 19.7 1.0
CG B:LEU57 4.1 21.1 1.0
C1 B:PFB378 4.2 12.8 1.0
CG B:LEU116 4.2 21.4 1.0
F2 B:PFB378 4.7 14.8 1.0
CB B:LEU116 4.7 19.4 1.0
F6 B:PFB378 4.7 14.5 1.0
CG1 B:VAL294 4.8 16.0 1.0
CG2 B:VAL294 4.9 16.5 1.0

Fluorine binding site 9 out of 10 in 4nfh

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Fluorine binding site 9 out of 10 in the V207A 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 V207A 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:16.8
occ:1.00
 F5 B:PFB378 0.0 16.8 1.0
C5 B:PFB378 1.4 15.0 1.0
C4 B:PFB378 2.3 14.3 1.0
C6 B:PFB378 2.4 12.8 1.0
F6 B:PFB378 2.7 14.5 1.0
F4 B:PFB378 2.7 16.6 1.0
CD1 B:LEU57 3.1 20.3 1.0
CZ B:PHE140 3.3 13.5 1.0
CD1 B:LEU141 3.4 13.8 1.0
C3 B:PFB378 3.6 14.7 1.0
C1 B:PFB378 3.7 12.8 1.0
CE1 B:PHE140 3.7 13.8 1.0
CD2 B:LEU141 3.8 17.4 1.0
CG B:LEU141 4.0 13.8 1.0
C2 B:PFB378 4.1 14.8 1.0
CE2 B:PHE140 4.3 14.3 1.0
CG B:LEU57 4.4 21.1 1.0
CB B:SER48 4.4 11.6 1.0
O B:HOH776 4.4 43.5 1.0
CD2 B:LEU57 4.5 19.6 1.0
F3 B:PFB378 4.7 15.5 1.0
O B:HOH755 4.7 34.9 1.0
C7 B:PFB378 4.9 12.8 1.0
CG B:LEU116 4.9 21.4 1.0
CD1 B:PHE140 5.0 12.0 1.0
O B:SER48 5.0 12.4 1.0
CD2 B:LEU116 5.0 19.7 1.0

Fluorine binding site 10 out of 10 in 4nfh

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Fluorine binding site 10 out of 10 in the V207A 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 V207A 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:14.5
occ:1.00
 F6 B:PFB378 0.0 14.5 1.0
C6 B:PFB378 1.3 12.8 1.0
C5 B:PFB378 2.3 15.0 1.0
C1 B:PFB378 2.4 12.8 1.0
F5 B:PFB378 2.7 16.8 1.0
C7 B:PFB378 2.8 12.8 1.0
O1 B:PFB378 3.2 12.3 1.0
CD1 B:LEU141 3.2 13.8 1.0
CB B:SER48 3.2 11.6 1.0
NE2 B:HIS67 3.3 11.6 1.0
CE1 B:HIS67 3.4 10.8 1.0
CD2 B:HIS67 3.5 12.5 1.0
C4 B:PFB378 3.6 14.3 1.0
C2 B:PFB378 3.6 14.8 1.0
ND1 B:HIS67 3.7 11.0 1.0
CG B:HIS67 3.7 11.0 1.0
OG B:SER48 3.7 11.2 1.0
C3 B:PFB378 4.1 14.7 1.0
CZ B:PHE140 4.1 13.5 1.0
ZN B:ZN375 4.1 12.8 1.0
CE2 B:PHE140 4.3 14.3 1.0
CG B:LEU141 4.6 13.8 1.0
CA B:SER48 4.6 11.8 1.0
F4 B:PFB378 4.7 16.6 1.0
CB B:HIS67 4.7 11.3 1.0
F2 B:PFB378 4.7 14.8 1.0
CD1 B:PHE93 4.8 11.1 1.0
C B:SER48 4.8 12.3 1.0
CE1 B:PHE93 4.8 11.8 1.0
CD1 B:LEU57 4.9 20.3 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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