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Fluorine in PDB 3oq6: Horse Liver Alcohol Dehydrogenase A317C Mutant Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol

Enzymatic activity of Horse Liver Alcohol Dehydrogenase A317C Mutant Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase A317C Mutant Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase A317C Mutant Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol, PDB code: 3oq6 was solved by B.V.Plapp, T.J.Herdendorf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.85 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.340, 51.310, 92.210, 91.98, 102.95, 110.11
R / Rfree (%) 13.5 / 16.2

Other elements in 3oq6:

The structure of Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol (pdb code 3oq6). 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 A317C Mutant Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol, PDB code: 3oq6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 3oq6

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Fluorine binding site 1 out of 10 in the Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant 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:12.2
occ:1.00
 F2 A:PFB378 0.0 12.2 1.0
C2 A:PFB378 1.3 10.7 1.0
C3 A:PFB378 2.3 11.8 1.0
C1 A:PFB378 2.4 10.9 1.0
F3 A:PFB378 2.7 13.0 1.0
C7N A:NAJ377 2.8 8.8 1.0
C7 A:PFB378 2.9 10.4 1.0
O7N A:NAJ377 3.0 9.1 1.0
C3N A:NAJ377 3.0 9.1 1.0
C2N A:NAJ377 3.3 8.2 1.0
N7N A:NAJ377 3.4 9.3 1.0
C4 A:PFB378 3.6 12.8 1.0
C6 A:PFB378 3.6 12.2 1.0
CG2 A:VAL294 3.7 13.5 1.0
CD1 A:ILE318 3.7 15.1 1.0
O1 A:PFB378 3.8 10.5 1.0
C4N A:NAJ377 3.8 9.2 1.0
C5 A:PFB378 4.1 12.5 1.0
N1N A:NAJ377 4.3 8.6 1.0
OG A:SER48 4.5 10.0 1.0
CE1 A:PHE93 4.6 10.2 1.0
CG2 A:ILE318 4.6 10.4 1.0
CD2 B:LEU309 4.6 16.3 1.0
CD2 A:LEU116 4.7 18.0 1.0
F4 A:PFB378 4.7 14.3 1.0
C5N A:NAJ377 4.7 9.6 1.0
F6 A:PFB378 4.7 12.5 1.0
CZ A:PHE93 4.8 10.4 1.0
C6N A:NAJ377 4.9 8.9 1.0
CG1 A:ILE318 5.0 11.2 1.0

Fluorine binding site 2 out of 10 in 3oq6

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Fluorine binding site 2 out of 10 in the Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant 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:13.0
occ:1.00
 F3 A:PFB378 0.0 13.0 1.0
C3 A:PFB378 1.3 11.8 1.0
C4 A:PFB378 2.4 12.8 1.0
C2 A:PFB378 2.4 10.7 1.0
F2 A:PFB378 2.7 12.2 1.0
F4 A:PFB378 2.7 14.3 1.0
CG2 A:VAL294 3.5 13.5 1.0
CD1 A:ILE318 3.5 15.1 1.0
CD2 B:LEU309 3.5 16.3 1.0
C5 A:PFB378 3.6 12.5 1.0
C1 A:PFB378 3.7 10.9 1.0
CD2 A:LEU116 3.7 18.0 1.0
C6 A:PFB378 4.1 12.2 1.0
O A:HOH681 4.2 23.8 1.0
CB A:VAL294 4.7 11.1 1.0
CG1 A:VAL294 4.7 13.5 1.0
F5 A:PFB378 4.7 14.4 1.0
CG B:LEU309 4.8 13.5 1.0
CG A:LEU116 4.8 17.8 1.0
CE B:MET306 4.8 18.5 1.0
CG1 A:ILE318 4.9 11.2 1.0
C7 A:PFB378 4.9 10.4 1.0

Fluorine binding site 3 out of 10 in 3oq6

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Fluorine binding site 3 out of 10 in the Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant 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:14.3
occ:1.00
 F4 A:PFB378 0.0 14.3 1.0
C4 A:PFB378 1.4 12.8 1.0
C3 A:PFB378 2.4 11.8 1.0
C5 A:PFB378 2.4 12.5 1.0
F3 A:PFB378 2.7 13.0 1.0
F5 A:PFB378 2.7 14.4 1.0
CD1 A:LEU57 3.2 16.7 0.4
CD2 A:LEU57 3.3 14.8 0.6
CD2 A:LEU57 3.6 15.7 0.4
C2 A:PFB378 3.6 10.7 1.0
C6 A:PFB378 3.6 12.2 1.0
O A:HOH681 3.7 23.8 1.0
CD1 A:LEU57 3.7 13.5 0.6
CD2 A:LEU116 3.9 18.0 1.0
CG A:LEU57 4.0 13.9 0.4
O A:HOH682 4.0 35.7 1.0
CG A:LEU57 4.1 12.9 0.6
CG A:LEU116 4.1 17.8 1.0
C1 A:PFB378 4.1 10.9 1.0
CB A:LEU116 4.6 16.7 1.0
F2 A:PFB378 4.7 12.2 1.0
F6 A:PFB378 4.7 12.5 1.0
O A:LEU116 4.8 20.4 1.0
CG2 A:VAL294 4.8 13.5 1.0
CD2 A:LEU141 4.9 15.1 1.0
CG1 A:VAL294 4.9 13.5 1.0

Fluorine binding site 4 out of 10 in 3oq6

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Fluorine binding site 4 out of 10 in the Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant 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:14.4
occ:1.00
 F5 A:PFB378 0.0 14.4 1.0
C5 A:PFB378 1.3 12.5 1.0
C6 A:PFB378 2.3 12.2 1.0
C4 A:PFB378 2.4 12.8 1.0
F6 A:PFB378 2.7 12.5 1.0
F4 A:PFB378 2.7 14.3 1.0
CD2 A:LEU57 2.8 15.7 0.4
CD1 A:LEU57 3.2 13.5 0.6
CZ A:PHE140 3.3 11.5 1.0
CD1 A:LEU141 3.3 12.3 1.0
C3 A:PFB378 3.6 11.8 1.0
C1 A:PFB378 3.6 10.9 1.0
CD2 A:LEU141 3.7 15.1 1.0
CE1 A:PHE140 3.7 11.5 1.0
CG A:LEU141 3.9 12.0 1.0
CG A:LEU57 4.0 13.9 0.4
C2 A:PFB378 4.1 10.7 1.0
CD1 A:LEU57 4.2 16.7 0.4
CE2 A:PHE140 4.3 11.8 1.0
CG A:LEU57 4.4 12.9 0.6
CD2 A:LEU57 4.4 14.8 0.6
CB A:SER48 4.5 9.8 1.0
O A:HOH863 4.7 47.0 1.0
F3 A:PFB378 4.7 13.0 1.0
CG A:LEU116 4.9 17.8 1.0
C7 A:PFB378 4.9 10.4 1.0
CD2 A:LEU116 4.9 18.0 1.0
CD1 A:PHE140 4.9 11.0 1.0
OG A:SER48 5.0 10.0 1.0

Fluorine binding site 5 out of 10 in 3oq6

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Fluorine binding site 5 out of 10 in the Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant 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:12.5
occ:1.00
 F6 A:PFB378 0.0 12.5 1.0
C6 A:PFB378 1.3 12.2 1.0
C5 A:PFB378 2.3 12.5 1.0
C1 A:PFB378 2.3 10.9 1.0
F5 A:PFB378 2.7 14.4 1.0
C7 A:PFB378 2.8 10.4 1.0
O1 A:PFB378 3.2 10.5 1.0
CD1 A:LEU141 3.2 12.3 1.0
CB A:SER48 3.2 9.8 1.0
NE2 A:HIS67 3.3 10.3 1.0
CE1 A:HIS67 3.4 8.9 1.0
CD2 A:HIS67 3.5 9.8 1.0
C4 A:PFB378 3.6 12.8 1.0
C2 A:PFB378 3.6 10.7 1.0
ND1 A:HIS67 3.7 9.7 1.0
OG A:SER48 3.7 10.0 1.0
CG A:HIS67 3.7 9.6 1.0
CZ A:PHE140 4.0 11.5 1.0
ZN A:ZN375 4.1 10.6 1.0
C3 A:PFB378 4.1 11.8 1.0
CE2 A:PHE140 4.2 11.8 1.0
CG A:LEU141 4.5 12.0 1.0
CA A:SER48 4.6 10.2 1.0
F4 A:PFB378 4.7 14.3 1.0
CB A:HIS67 4.7 8.5 1.0
F2 A:PFB378 4.7 12.2 1.0
CD1 A:LEU57 4.7 13.5 0.6
CD2 A:LEU57 4.8 15.7 0.4
C A:SER48 4.8 10.3 1.0
CD1 A:PHE93 4.8 9.2 1.0
CE1 A:PHE93 4.8 10.2 1.0

Fluorine binding site 6 out of 10 in 3oq6

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Fluorine binding site 6 out of 10 in the Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant 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
 F2 B:PFB378 0.0 14.5 1.0
C2 B:PFB378 1.3 13.5 1.0
C3 B:PFB378 2.3 13.8 1.0
C1 B:PFB378 2.4 13.4 1.0
F3 B:PFB378 2.7 15.2 1.0
C7N B:NAJ377 2.9 10.7 1.0
C7 B:PFB378 2.9 13.2 1.0
C3N B:NAJ377 3.0 10.8 1.0
O7N B:NAJ377 3.1 11.1 1.0
C2N B:NAJ377 3.4 10.3 1.0
N7N B:NAJ377 3.4 10.6 1.0
C4 B:PFB378 3.6 15.6 1.0
C6 B:PFB378 3.6 13.0 1.0
CD1 B:ILE318 3.7 17.5 1.0
CG2 B:VAL294 3.7 15.6 1.0
O1 B:PFB378 3.8 12.9 1.0
C4N B:NAJ377 3.8 11.7 1.0
C5 B:PFB378 4.1 14.9 1.0
N1N B:NAJ377 4.3 10.1 1.0
OG B:SER48 4.4 11.7 1.0
CE1 B:PHE93 4.6 12.1 1.0
F4 B:PFB378 4.6 16.2 1.0
CG2 B:ILE318 4.6 12.6 1.0
CD2 B:LEU116 4.7 21.2 1.0
F6 B:PFB378 4.7 13.7 1.0
CD2 A:LEU309 4.7 15.2 0.7
C5N B:NAJ377 4.7 10.6 1.0
CZ B:PHE93 4.8 13.2 1.0
C6N B:NAJ377 5.0 10.2 1.0
CG1 B:ILE318 5.0 12.6 1.0

Fluorine binding site 7 out of 10 in 3oq6

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Fluorine binding site 7 out of 10 in the Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant 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:15.2
occ:1.00
 F3 B:PFB378 0.0 15.2 1.0
C3 B:PFB378 1.3 13.8 1.0
C4 B:PFB378 2.3 15.6 1.0
C2 B:PFB378 2.4 13.5 1.0
F2 B:PFB378 2.7 14.5 1.0
F4 B:PFB378 2.7 16.2 1.0
CG2 B:VAL294 3.5 15.6 1.0
C5 B:PFB378 3.6 14.9 1.0
CD1 B:ILE318 3.6 17.5 1.0
C1 B:PFB378 3.6 13.4 1.0
CD2 A:LEU309 3.6 15.2 0.7
CD2 B:LEU116 3.8 21.2 1.0
C6 B:PFB378 4.1 13.0 1.0
CG1 B:VAL294 4.6 15.1 1.0
CB B:VAL294 4.6 13.6 1.0
F5 B:PFB378 4.7 15.7 1.0
CG A:LEU309 4.8 12.4 0.7
CG B:LEU116 4.9 21.4 1.0
C7 B:PFB378 4.9 13.2 1.0
CG1 B:ILE318 5.0 12.6 1.0

Fluorine binding site 8 out of 10 in 3oq6

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Fluorine binding site 8 out of 10 in the Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant 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:16.2
occ:1.00
 F4 B:PFB378 0.0 16.2 1.0
C4 B:PFB378 1.3 15.6 1.0
C3 B:PFB378 2.3 13.8 1.0
C5 B:PFB378 2.4 14.9 1.0
F3 B:PFB378 2.7 15.2 1.0
F5 B:PFB378 2.7 15.7 1.0
CD2 B:LEU57 3.3 19.9 1.0
C2 B:PFB378 3.6 13.5 1.0
C6 B:PFB378 3.6 13.0 1.0
CD1 B:LEU57 3.6 20.8 1.0
O B:HOH776 3.6 40.1 1.0
CD2 B:LEU116 4.0 21.2 1.0
CG B:LEU57 4.1 19.9 1.0
C1 B:PFB378 4.1 13.4 1.0
CG B:LEU116 4.2 21.4 1.0
F2 B:PFB378 4.6 14.5 1.0
F6 B:PFB378 4.7 13.7 1.0
CB B:LEU116 4.7 19.9 1.0
CG1 B:VAL294 4.8 15.1 1.0
CG2 B:VAL294 4.9 15.6 1.0

Fluorine binding site 9 out of 10 in 3oq6

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Fluorine binding site 9 out of 10 in the Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant 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:15.7
occ:1.00
 F5 B:PFB378 0.0 15.7 1.0
C5 B:PFB378 1.3 14.9 1.0
C4 B:PFB378 2.3 15.6 1.0
C6 B:PFB378 2.4 13.0 1.0
F6 B:PFB378 2.7 13.7 1.0
F4 B:PFB378 2.7 16.2 1.0
CD1 B:LEU57 3.1 20.8 1.0
CZ B:PHE140 3.3 14.6 1.0
CD1 B:LEU141 3.4 15.0 1.0
C3 B:PFB378 3.6 13.8 1.0
C1 B:PFB378 3.6 13.4 1.0
CE1 B:PHE140 3.8 13.6 1.0
CD2 B:LEU141 3.8 16.9 1.0
CG B:LEU141 4.0 13.2 1.0
C2 B:PFB378 4.1 13.5 1.0
CE2 B:PHE140 4.3 14.2 1.0
O B:HOH776 4.3 40.1 1.0
CG B:LEU57 4.4 19.9 1.0
CB B:SER48 4.4 11.6 1.0
CD2 B:LEU57 4.5 19.9 1.0
F3 B:PFB378 4.7 15.2 1.0
O B:HOH755 4.8 35.0 1.0
C7 B:PFB378 4.9 13.2 1.0
CG B:LEU116 5.0 21.4 1.0
O B:SER48 5.0 13.0 1.0
CD1 B:PHE140 5.0 13.6 1.0
OG B:SER48 5.0 11.7 1.0
CD2 B:LEU116 5.0 21.2 1.0

Fluorine binding site 10 out of 10 in 3oq6

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Fluorine binding site 10 out of 10 in the Horse Liver Alcohol Dehydrogenase A317C Mutant 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 Liver Alcohol Dehydrogenase A317C Mutant 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:13.7
occ:1.00
 F6 B:PFB378 0.0 13.7 1.0
C6 B:PFB378 1.3 13.0 1.0
C5 B:PFB378 2.3 14.9 1.0
C1 B:PFB378 2.3 13.4 1.0
F5 B:PFB378 2.7 15.7 1.0
C7 B:PFB378 2.8 13.2 1.0
O1 B:PFB378 3.2 12.9 1.0
CD1 B:LEU141 3.2 15.0 1.0
CB B:SER48 3.2 11.6 1.0
NE2 B:HIS67 3.2 12.1 1.0
CE1 B:HIS67 3.4 11.0 1.0
CD2 B:HIS67 3.5 10.8 1.0
C4 B:PFB378 3.6 15.6 1.0
C2 B:PFB378 3.6 13.5 1.0
ND1 B:HIS67 3.7 11.7 1.0
OG B:SER48 3.7 11.7 1.0
CG B:HIS67 3.7 11.0 1.0
ZN B:ZN375 4.0 12.5 1.0
C3 B:PFB378 4.1 13.8 1.0
CZ B:PHE140 4.1 14.6 1.0
CE2 B:PHE140 4.3 14.2 1.0
CG B:LEU141 4.6 13.2 1.0
CA B:SER48 4.6 12.1 1.0
F4 B:PFB378 4.7 16.2 1.0
F2 B:PFB378 4.7 14.5 1.0
CB B:HIS67 4.7 11.2 1.0
CD1 B:PHE93 4.8 10.6 1.0
C B:SER48 4.8 12.6 1.0
CE1 B:PHE93 4.8 12.1 1.0
CD1 B:LEU57 4.9 20.8 1.0

Reference:

T.J.Herdendorf, B.V.Plapp. Origins of the High Catalytic Activity of Human Alcohol Dehydrogenase 4 Studied with Horse Liver A317C Alcohol Dehydrogenase. Chem.Biol.Interact V. 191 42 2011.
ISSN: ISSN 0009-2797
PubMed: 21184752
DOI: 10.1016/J.CBI.2010.12.015
Page generated: Wed Jul 31 21:21:21 2024

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