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Fluorine in PDB 5kjf: V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol

Enzymatic activity of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol

All present enzymatic activity of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol:
1.1.1.1;

Protein crystallography data

The structure of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol, PDB code: 5kjf 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) 20.00 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.200, 51.330, 92.530, 91.88, 103.06, 109.84
R / Rfree (%) 13.3 / 15.3

Other elements in 5kjf:

The structure of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol (pdb code 5kjf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol, PDB code: 5kjf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5kjf

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Fluorine binding site 1 out of 9 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:21.8
occ:0.80
 F1 A:ETF378 0.0 21.8 0.8
C1 A:ETF378 1.3 17.0 0.8
F1 A:ETF378 1.4 16.4 0.2
C1 A:ETF378 2.0 16.4 0.2
C2 A:ETF378 2.1 15.6 0.2
F3 A:ETF378 2.1 20.6 0.8
F2 A:ETF378 2.2 20.4 0.8
C2 A:ETF378 2.3 16.7 0.8
F2 A:ETF378 2.7 18.4 0.2
O A:ETF378 2.8 14.5 1.0
F3 A:ETF378 3.2 18.5 0.2
CG2 A:VAL294 3.3 15.2 1.0
C3N A:NAJ377 3.3 10.3 1.0
OG A:SER48 3.3 12.9 1.0
C2N A:NAJ377 3.4 9.8 1.0
C7N A:NAJ377 3.7 9.9 1.0
C4N A:NAJ377 3.7 11.1 1.0
N1N A:NAJ377 3.9 10.0 1.0
O7N A:NAJ377 4.0 10.7 1.0
CB A:SER48 4.2 12.2 1.0
C5N A:NAJ377 4.3 11.4 1.0
C6N A:NAJ377 4.4 10.4 1.0
N7N A:NAJ377 4.4 10.2 1.0
O2D A:NAJ377 4.6 11.2 1.0
CB A:VAL294 4.7 13.0 1.0
C1D A:NAJ377 4.7 10.1 1.0
ZN A:ZN375 4.8 15.8 0.8
CE1 A:PHE93 4.9 12.1 1.0

Fluorine binding site 2 out of 9 in 5kjf

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Fluorine binding site 2 out of 9 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:16.4
occ:0.20
 F1 A:ETF378 0.0 16.4 0.2
F3 A:ETF378 0.9 20.6 0.8
C1 A:ETF378 1.2 17.0 0.8
C1 A:ETF378 1.3 16.4 0.2
F1 A:ETF378 1.4 21.8 0.8
F2 A:ETF378 2.1 20.4 0.8
F2 A:ETF378 2.2 18.4 0.2
F3 A:ETF378 2.2 18.5 0.2
C2 A:ETF378 2.3 15.6 0.2
C2 A:ETF378 2.5 16.7 0.8
O A:ETF378 3.0 14.5 1.0
OG A:SER48 3.2 12.9 1.0
CB A:SER48 3.6 12.2 1.0
CG2 A:VAL294 3.6 15.2 1.0
CD2 A:LEU57 4.1 17.9 1.0
CD1 A:LEU116 4.4 20.7 1.0
C3N A:NAJ377 4.6 10.3 1.0
C2N A:NAJ377 4.6 9.8 1.0
CB A:VAL294 4.8 13.0 1.0
O2D A:NAJ377 4.8 11.2 1.0
CD2 A:LEU116 4.9 20.6 1.0
C4N A:NAJ377 4.9 11.1 1.0
CA A:SER48 4.9 11.8 1.0
N1N A:NAJ377 4.9 10.0 1.0
CD1 A:LEU141 4.9 15.5 1.0
ZN A:ZN375 5.0 15.8 0.8

Fluorine binding site 3 out of 9 in 5kjf

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Fluorine binding site 3 out of 9 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:20.4
occ:0.80
 F2 A:ETF378 0.0 20.4 0.8
F2 A:ETF378 0.9 18.4 0.2
C1 A:ETF378 1.3 17.0 0.8
C1 A:ETF378 1.6 16.4 0.2
F1 A:ETF378 2.1 16.4 0.2
F3 A:ETF378 2.2 20.6 0.8
C2 A:ETF378 2.2 15.6 0.2
F1 A:ETF378 2.2 21.8 0.8
C2 A:ETF378 2.3 16.7 0.8
F3 A:ETF378 2.8 18.5 0.2
CE1 A:PHE93 3.3 12.1 1.0
O A:ETF378 3.6 14.5 1.0
CD2 A:LEU116 3.7 20.6 1.0
CD1 A:PHE93 3.8 11.5 1.0
CD1 A:LEU116 4.0 20.7 1.0
CZ A:PHE93 4.1 12.3 1.0
CD1 A:LEU141 4.2 15.5 1.0
O7N A:NAJ377 4.3 10.7 1.0
CG A:LEU116 4.5 18.4 1.0
CG2 A:ILE318 4.6 12.0 1.0
C7N A:NAJ377 4.6 9.9 1.0
C3N A:NAJ377 4.7 10.3 1.0
CD1 A:ILE318 4.8 15.5 1.0
C4N A:NAJ377 4.9 11.1 1.0
CG A:PHE93 4.9 10.9 1.0
OG A:SER48 4.9 12.9 1.0

Fluorine binding site 4 out of 9 in 5kjf

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Fluorine binding site 4 out of 9 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:18.4
occ:0.20
 F2 A:ETF378 0.0 18.4 0.2
F2 A:ETF378 0.9 20.4 0.8
C1 A:ETF378 1.3 16.4 0.2
C1 A:ETF378 1.6 17.0 0.8
F3 A:ETF378 1.9 20.6 0.8
F3 A:ETF378 2.2 18.5 0.2
F1 A:ETF378 2.2 16.4 0.2
C2 A:ETF378 2.3 15.6 0.2
C2 A:ETF378 2.4 16.7 0.8
F1 A:ETF378 2.7 21.8 0.8
CD1 A:LEU141 3.4 15.5 1.0
CE1 A:PHE93 3.4 12.1 1.0
O A:ETF378 3.6 14.5 1.0
CD1 A:PHE93 3.6 11.5 1.0
CD1 A:LEU116 3.9 20.7 1.0
CD2 A:LEU116 4.0 20.6 1.0
CZ A:PHE93 4.2 12.3 1.0
CG A:LEU116 4.5 18.4 1.0
CG A:PHE93 4.6 10.9 1.0
CG A:LEU141 4.6 14.3 1.0
CD2 A:LEU141 4.7 17.6 1.0
OG A:SER48 4.9 12.9 1.0
CD2 A:HIS67 5.0 14.9 1.0

Fluorine binding site 5 out of 9 in 5kjf

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Fluorine binding site 5 out of 9 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:20.6
occ:0.80
 F3 A:ETF378 0.0 20.6 0.8
F1 A:ETF378 0.9 16.4 0.2
C1 A:ETF378 0.9 16.4 0.2
C1 A:ETF378 1.3 17.0 0.8
F3 A:ETF378 1.3 18.5 0.2
F2 A:ETF378 1.9 18.4 0.2
F1 A:ETF378 2.1 21.8 0.8
F2 A:ETF378 2.2 20.4 0.8
C2 A:ETF378 2.2 15.6 0.2
C2 A:ETF378 2.4 16.7 0.8
O A:ETF378 2.9 14.5 1.0
OG A:SER48 3.2 12.9 1.0
CB A:SER48 3.3 12.2 1.0
CD2 A:LEU57 3.8 17.9 1.0
CD1 A:LEU141 4.2 15.5 1.0
CG2 A:VAL294 4.4 15.2 1.0
CD1 A:LEU116 4.4 20.7 1.0
CA A:SER48 4.7 11.8 1.0
NE2 A:HIS67 4.7 15.3 1.0
ZN A:ZN375 4.7 15.8 0.8
CE1 A:HIS67 5.0 12.7 1.0

Fluorine binding site 6 out of 9 in 5kjf

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Fluorine binding site 6 out of 9 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:18.5
occ:0.20
 F3 A:ETF378 0.0 18.5 0.2
C1 A:ETF378 1.3 16.4 0.2
F3 A:ETF378 1.3 20.6 0.8
C1 A:ETF378 2.1 17.0 0.8
F2 A:ETF378 2.2 18.4 0.2
F1 A:ETF378 2.2 16.4 0.2
C2 A:ETF378 2.4 15.6 0.2
C2 A:ETF378 2.4 16.7 0.8
F2 A:ETF378 2.8 20.4 0.8
O A:ETF378 2.8 14.5 1.0
CB A:SER48 3.2 12.2 1.0
F1 A:ETF378 3.2 21.8 0.8
CD1 A:LEU141 3.3 15.5 1.0
OG A:SER48 3.5 12.9 1.0
NE2 A:HIS67 3.6 15.3 1.0
CE1 A:HIS67 3.9 12.7 1.0
CD2 A:HIS67 3.9 14.9 1.0
CD2 A:LEU57 4.1 17.9 1.0
CZ A:PHE140 4.2 14.2 1.0
ZN A:ZN375 4.2 15.8 0.8
ND1 A:HIS67 4.3 12.1 1.0
CG A:HIS67 4.3 11.1 1.0
CE2 A:PHE140 4.5 14.4 1.0
CA A:SER48 4.6 11.8 1.0
CG A:LEU141 4.7 14.3 1.0
CE1 A:PHE93 4.9 12.1 1.0
CD1 A:PHE93 4.9 11.5 1.0
C A:SER48 4.9 11.6 1.0

Fluorine binding site 7 out of 9 in 5kjf

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Fluorine binding site 7 out of 9 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:29.8
occ:1.00
 F1 B:ETF378 0.0 29.8 1.0
C1 B:ETF378 1.3 23.5 1.0
F3 B:ETF378 2.1 29.5 1.0
F2 B:ETF378 2.2 27.5 1.0
C2 B:ETF378 2.3 21.4 1.0
O B:ETF378 2.8 19.4 1.0
C3N B:NAJ377 3.3 12.2 1.0
OG B:SER48 3.3 16.1 1.0
CG2 B:VAL294 3.3 17.6 1.0
C2N B:NAJ377 3.4 12.3 1.0
C7N B:NAJ377 3.7 12.8 1.0
C4N B:NAJ377 3.7 14.6 1.0
O7N B:NAJ377 3.9 12.9 1.0
N1N B:NAJ377 4.0 12.8 1.0
CB B:SER48 4.2 15.8 1.0
C5N B:NAJ377 4.4 14.3 1.0
N7N B:NAJ377 4.4 13.2 1.0
C6N B:NAJ377 4.4 13.6 1.0
O2D B:NAJ377 4.7 13.7 1.0
C1D B:NAJ377 4.8 12.8 1.0
CB B:VAL294 4.8 16.3 1.0
ZN B:ZN375 4.8 20.0 0.8
CE1 B:PHE93 4.9 14.1 1.0

Fluorine binding site 8 out of 9 in 5kjf

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Fluorine binding site 8 out of 9 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:27.5
occ:1.00
 F2 B:ETF378 0.0 27.5 1.0
C1 B:ETF378 1.3 23.5 1.0
F3 B:ETF378 2.1 29.5 1.0
F1 B:ETF378 2.2 29.8 1.0
C2 B:ETF378 2.3 21.4 1.0
CE1 B:PHE93 3.3 14.1 1.0
O B:ETF378 3.6 19.4 1.0
CD2 B:LEU116 3.7 25.1 1.0
CD1 B:PHE93 3.9 13.7 1.0
CD1 B:LEU116 4.0 25.1 1.0
CZ B:PHE93 4.1 14.8 1.0
CD1 B:LEU141 4.3 19.5 1.0
O7N B:NAJ377 4.3 12.9 1.0
CG B:LEU116 4.5 21.4 1.0
CG2 B:ILE318 4.6 14.5 1.0
C7N B:NAJ377 4.7 12.8 1.0
CD1 B:ILE318 4.8 17.9 1.0
C3N B:NAJ377 4.8 12.2 1.0
OG B:SER48 4.8 16.1 1.0
C4N B:NAJ377 4.9 14.6 1.0
CG B:PHE93 4.9 13.2 1.0

Fluorine binding site 9 out of 9 in 5kjf

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Fluorine binding site 9 out of 9 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:29.5
occ:1.00
 F3 B:ETF378 0.0 29.5 1.0
C1 B:ETF378 1.3 23.5 1.0
F1 B:ETF378 2.1 29.8 1.0
F2 B:ETF378 2.1 27.5 1.0
C2 B:ETF378 2.3 21.4 1.0
O B:ETF378 2.9 19.4 1.0
OG B:SER48 3.2 16.1 1.0
CB B:SER48 3.3 15.8 1.0
CD2 B:LEU57 3.9 24.4 1.0
CD1 B:LEU141 4.2 19.5 1.0
CG2 B:VAL294 4.5 17.6 1.0
CD1 B:LEU116 4.5 25.1 1.0
NE2 B:HIS67 4.6 18.7 1.0
CA B:SER48 4.7 15.5 1.0
ZN B:ZN375 4.7 20.0 0.8
CE1 B:HIS67 5.0 16.1 1.0

Reference:

K.K.Shanmuganatham, R.S.Wallace, A.Ting-I Lee, B.V.Plapp. Contribution of Buried Distal Amino Acid Residues in Horse Liver Alcohol Dehydrogenase to Structure and Catalysis. Protein Sci. V. 27 750 2018.
ISSN: ESSN 1469-896X
PubMed: 29271062
DOI: 10.1002/PRO.3370
Page generated: Thu Aug 1 11:06:54 2024

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