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Fluorine in PDB 5cdg: I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

Enzymatic activity of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

All present enzymatic activity of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 5cdg was solved by B.V.Plapp, K.Shanmuganatham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.260, 51.380, 92.390, 91.75, 103.10, 109.36
R / Rfree (%) 14.2 / 18.7

Other elements in 5cdg:

The structure of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol (pdb code 5cdg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 5cdg:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 5cdg

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Fluorine binding site 1 out of 10 in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:19.4
occ:1.00
F2 A:PFB404 0.0 19.4 1.0
C2 A:PFB404 1.3 17.1 1.0
C3 A:PFB404 2.3 18.1 1.0
C1 A:PFB404 2.4 18.5 1.0
F3 A:PFB404 2.6 19.6 1.0
C7N A:NAJ403 2.9 13.2 1.0
C7 A:PFB404 2.9 17.9 1.0
O7N A:NAJ403 3.0 15.3 1.0
C3N A:NAJ403 3.1 13.3 1.0
C2N A:NAJ403 3.4 13.7 1.0
N7N A:NAJ403 3.5 13.6 1.0
C4 A:PFB404 3.6 20.2 1.0
C6 A:PFB404 3.6 19.1 1.0
CG2 A:VAL294 3.8 18.3 1.0
C4N A:NAJ403 3.8 15.4 1.0
O1 A:PFB404 3.8 16.0 1.0
CD1 A:ILE318 3.8 21.4 1.0
C5 A:PFB404 4.1 18.8 1.0
N1N A:NAJ403 4.3 12.6 1.0
OG A:SER48 4.5 14.7 1.0
CE1 A:PHE93 4.5 14.3 1.0
CD2 A:LEU116 4.6 26.0 1.0
CG2 A:ILE318 4.6 16.6 1.0
F4 A:PFB404 4.6 20.7 1.0
F6 A:PFB404 4.7 19.6 1.0
CD2 B:LEU309 4.7 25.9 1.0
C5N A:NAJ403 4.8 14.3 1.0
CZ A:PHE93 4.8 14.8 1.0
C6N A:NAJ403 5.0 12.8 1.0

Fluorine binding site 2 out of 10 in 5cdg

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Fluorine binding site 2 out of 10 in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:19.6
occ:1.00
F3 A:PFB404 0.0 19.6 1.0
C3 A:PFB404 1.3 18.1 1.0
C2 A:PFB404 2.3 17.1 1.0
C4 A:PFB404 2.3 20.2 1.0
F2 A:PFB404 2.6 19.4 1.0
F4 A:PFB404 2.7 20.7 1.0
CG2 A:VAL294 3.5 18.3 1.0
C5 A:PFB404 3.6 18.8 1.0
C1 A:PFB404 3.6 18.5 1.0
CD1 A:ILE318 3.6 21.4 1.0
CD2 B:LEU309 3.7 25.9 1.0
CD2 A:LEU116 3.7 26.0 1.0
C6 A:PFB404 4.1 19.1 1.0
O A:HOH975 4.1 39.5 1.0
CB A:VAL294 4.6 15.9 1.0
CG1 A:VAL294 4.7 18.6 1.0
F5 A:PFB404 4.7 20.0 1.0
CG A:LEU116 4.8 23.5 1.0
CG B:LEU309 4.8 20.4 1.0
C7 A:PFB404 4.9 17.9 1.0
CE B:MET306 4.9 27.1 1.0
CG1 A:ILE318 4.9 17.0 1.0

Fluorine binding site 3 out of 10 in 5cdg

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Fluorine binding site 3 out of 10 in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:20.7
occ:1.00
F4 A:PFB404 0.0 20.7 1.0
C4 A:PFB404 1.3 20.2 1.0
C5 A:PFB404 2.3 18.8 1.0
C3 A:PFB404 2.4 18.1 1.0
F3 A:PFB404 2.7 19.6 1.0
F5 A:PFB404 2.7 20.0 1.0
CD2 A:LEU57 3.2 42.3 1.0
C2 A:PFB404 3.6 17.1 1.0
C6 A:PFB404 3.6 19.1 1.0
CD1 A:LEU57 3.7 26.7 1.0
O A:HOH975 3.8 39.5 1.0
CG A:LEU57 3.9 31.1 1.0
CD2 A:LEU116 3.9 26.0 1.0
O A:HOH763 4.0 41.4 1.0
C1 A:PFB404 4.1 18.5 1.0
CG A:LEU116 4.1 23.5 1.0
CB A:LEU116 4.5 22.5 1.0
F2 A:PFB404 4.6 19.4 1.0
F6 A:PFB404 4.7 19.6 1.0
O A:LEU116 4.8 26.4 1.0
CG2 A:VAL294 4.8 18.3 1.0
CD2 A:LEU141 4.9 20.3 1.0
CG1 A:VAL294 5.0 18.6 1.0

Fluorine binding site 4 out of 10 in 5cdg

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Fluorine binding site 4 out of 10 in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:20.0
occ:1.00
F5 A:PFB404 0.0 20.0 1.0
C5 A:PFB404 1.3 18.8 1.0
C6 A:PFB404 2.3 19.1 1.0
C4 A:PFB404 2.4 20.2 1.0
F6 A:PFB404 2.6 19.6 1.0
F4 A:PFB404 2.7 20.7 1.0
CD1 A:LEU57 3.2 26.7 1.0
CZ A:PHE140 3.2 16.1 1.0
CD1 A:LEU141 3.3 17.9 1.0
C1 A:PFB404 3.6 18.5 1.0
C3 A:PFB404 3.6 18.1 1.0
CD2 A:LEU141 3.7 20.3 1.0
CE1 A:PHE140 3.7 16.2 1.0
CG A:LEU141 3.9 16.8 1.0
CD2 A:LEU57 3.9 42.3 1.0
C2 A:PFB404 4.1 17.1 1.0
CG A:LEU57 4.1 31.1 1.0
CE2 A:PHE140 4.2 18.4 1.0
CB A:SER48 4.5 16.1 1.0
F3 A:PFB404 4.7 19.6 1.0
C7 A:PFB404 4.8 17.9 1.0
CG A:LEU116 4.9 23.5 1.0
CD1 A:PHE140 4.9 16.0 1.0
CD2 A:LEU116 5.0 26.0 1.0

Fluorine binding site 5 out of 10 in 5cdg

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Fluorine binding site 5 out of 10 in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:19.6
occ:1.00
F6 A:PFB404 0.0 19.6 1.0
C6 A:PFB404 1.3 19.1 1.0
C1 A:PFB404 2.3 18.5 1.0
C5 A:PFB404 2.3 18.8 1.0
F5 A:PFB404 2.6 20.0 1.0
C7 A:PFB404 2.8 17.9 1.0
O1 A:PFB404 3.2 16.0 1.0
CD1 A:LEU141 3.2 17.9 1.0
CB A:SER48 3.2 16.1 1.0
NE2 A:HIS67 3.3 14.7 1.0
CE1 A:HIS67 3.4 16.9 1.0
CD2 A:HIS67 3.5 14.8 1.0
C4 A:PFB404 3.6 20.2 1.0
C2 A:PFB404 3.6 17.1 1.0
ND1 A:HIS67 3.7 16.4 1.0
CG A:HIS67 3.7 14.2 1.0
OG A:SER48 3.8 14.7 1.0
CZ A:PHE140 4.0 16.1 1.0
C3 A:PFB404 4.1 18.1 1.0
ZN A:ZN401 4.1 17.5 1.0
CE2 A:PHE140 4.2 18.4 1.0
CG A:LEU141 4.5 16.8 1.0
CA A:SER48 4.6 15.1 1.0
F4 A:PFB404 4.7 20.7 1.0
CB A:HIS67 4.7 14.3 1.0
CD1 A:LEU57 4.7 26.7 1.0
F2 A:PFB404 4.7 19.4 1.0
CD1 A:PHE93 4.7 14.7 1.0
C A:SER48 4.8 14.8 1.0
CE1 A:PHE93 4.8 14.3 1.0

Fluorine binding site 6 out of 10 in 5cdg

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Fluorine binding site 6 out of 10 in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:21.6
occ:1.00
F2 B:PFB404 0.0 21.6 1.0
C2 B:PFB404 1.3 23.1 1.0
C3 B:PFB404 2.3 21.2 1.0
C1 B:PFB404 2.4 19.6 1.0
F3 B:PFB404 2.7 22.4 1.0
C7N B:NAJ403 2.8 17.4 1.0
C7 B:PFB404 2.9 18.8 1.0
O7N B:NAJ403 3.0 17.2 1.0
C3N B:NAJ403 3.0 16.5 1.0
C2N B:NAJ403 3.3 16.3 1.0
N7N B:NAJ403 3.4 16.1 1.0
C4 B:PFB404 3.6 22.8 1.0
C6 B:PFB404 3.7 20.0 1.0
O1 B:PFB404 3.7 18.1 1.0
CD1 B:ILE318 3.7 22.6 1.0
C4N B:NAJ403 3.8 17.6 1.0
CG2 B:VAL294 3.8 21.6 1.0
C5 B:PFB404 4.1 22.1 1.0
N1N B:NAJ403 4.3 16.0 1.0
OG B:SER48 4.5 17.3 1.0
CE1 B:PHE93 4.5 16.9 1.0
CG2 B:ILE318 4.6 18.6 1.0
CD2 B:LEU116 4.6 27.1 1.0
F4 B:PFB404 4.7 24.1 1.0
CZ B:PHE93 4.7 18.7 1.0
C5N B:NAJ403 4.7 17.3 1.0
F6 B:PFB404 4.8 22.1 1.0
CD2 A:LEU309 4.8 19.7 0.7
CG1 B:ILE318 4.9 17.0 1.0
C6N B:NAJ403 4.9 15.8 1.0

Fluorine binding site 7 out of 10 in 5cdg

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Fluorine binding site 7 out of 10 in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:22.4
occ:1.00
F3 B:PFB404 0.0 22.4 1.0
C3 B:PFB404 1.3 21.2 1.0
C4 B:PFB404 2.4 22.8 1.0
C2 B:PFB404 2.4 23.1 1.0
F2 B:PFB404 2.7 21.6 1.0
F4 B:PFB404 2.7 24.1 1.0
CG2 B:VAL294 3.4 21.6 1.0
CD1 B:ILE318 3.6 22.6 1.0
C5 B:PFB404 3.6 22.1 1.0
C1 B:PFB404 3.6 19.6 1.0
CD2 A:LEU309 3.7 19.7 0.7
CD2 B:LEU116 3.7 27.1 1.0
C6 B:PFB404 4.1 20.0 1.0
CG1 B:VAL294 4.5 19.9 1.0
CB B:VAL294 4.6 19.5 1.0
F5 B:PFB404 4.7 23.2 1.0
CG A:LEU309 4.8 16.5 0.7
CG B:LEU116 4.8 28.0 1.0
C7 B:PFB404 4.9 18.8 1.0
CG1 B:ILE318 4.9 17.0 1.0
CE A:MET306 5.0 37.8 1.0

Fluorine binding site 8 out of 10 in 5cdg

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Fluorine binding site 8 out of 10 in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:24.1
occ:1.00
F4 B:PFB404 0.0 24.1 1.0
C4 B:PFB404 1.3 22.8 1.0
C5 B:PFB404 2.4 22.1 1.0
C3 B:PFB404 2.4 21.2 1.0
F3 B:PFB404 2.7 22.4 1.0
F5 B:PFB404 2.7 23.2 1.0
CD2 B:LEU57 3.2 30.9 1.0
CD1 B:LEU57 3.6 30.9 1.0
C2 B:PFB404 3.6 23.1 1.0
C6 B:PFB404 3.6 20.0 1.0
O B:HOH786 3.8 49.8 1.0
CD2 B:LEU116 3.9 27.1 1.0
CG B:LEU57 4.0 33.5 1.0
C1 B:PFB404 4.1 19.6 1.0
CG B:LEU116 4.2 28.0 1.0
F2 B:PFB404 4.7 21.6 1.0
F6 B:PFB404 4.7 22.1 1.0
CB B:LEU116 4.7 27.6 1.0
CG1 B:VAL294 4.7 19.9 1.0
CG2 B:VAL294 4.8 21.6 1.0

Fluorine binding site 9 out of 10 in 5cdg

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Fluorine binding site 9 out of 10 in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:23.2
occ:1.00
F5 B:PFB404 0.0 23.2 1.0
C5 B:PFB404 1.3 22.1 1.0
C4 B:PFB404 2.3 22.8 1.0
C6 B:PFB404 2.4 20.0 1.0
F4 B:PFB404 2.7 24.1 1.0
F6 B:PFB404 2.8 22.1 1.0
CD1 B:LEU57 3.1 30.9 1.0
CZ B:PHE140 3.3 22.6 1.0
CD1 B:LEU141 3.4 23.0 1.0
C3 B:PFB404 3.6 21.2 1.0
C1 B:PFB404 3.7 19.6 1.0
CE1 B:PHE140 3.8 20.6 1.0
CD2 B:LEU141 3.9 23.4 1.0
CG B:LEU141 4.1 19.6 1.0
C2 B:PFB404 4.1 23.1 1.0
CE2 B:PHE140 4.3 23.9 1.0
CG B:LEU57 4.3 33.5 1.0
CD2 B:LEU57 4.4 30.9 1.0
CB B:SER48 4.4 17.3 1.0
O B:HOH786 4.4 49.8 1.0
F3 B:PFB404 4.7 22.4 1.0
O B:HOH723 4.8 44.4 1.0
O B:SER48 4.9 20.3 1.0
C7 B:PFB404 4.9 18.8 1.0
CD2 B:LEU116 4.9 27.1 1.0
CD1 B:PHE140 5.0 19.3 1.0
CG B:LEU116 5.0 28.0 1.0
OG B:SER48 5.0 17.3 1.0

Fluorine binding site 10 out of 10 in 5cdg

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Fluorine binding site 10 out of 10 in the I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of I220F Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:22.1
occ:1.00
F6 B:PFB404 0.0 22.1 1.0
C6 B:PFB404 1.3 20.0 1.0
C5 B:PFB404 2.4 22.1 1.0
C1 B:PFB404 2.4 19.6 1.0
F5 B:PFB404 2.8 23.2 1.0
C7 B:PFB404 2.8 18.8 1.0
O1 B:PFB404 3.1 18.1 1.0
CD1 B:LEU141 3.2 23.0 1.0
CB B:SER48 3.2 17.3 1.0
NE2 B:HIS67 3.3 17.2 1.0
CE1 B:HIS67 3.3 17.1 1.0
CD2 B:HIS67 3.5 17.6 1.0
C4 B:PFB404 3.6 22.8 1.0
C2 B:PFB404 3.6 23.1 1.0
ND1 B:HIS67 3.6 19.1 1.0
CG B:HIS67 3.7 17.1 1.0
OG B:SER48 3.7 17.3 1.0
ZN B:ZN401 4.0 20.1 1.0
CZ B:PHE140 4.1 22.6 1.0
C3 B:PFB404 4.1 21.2 1.0
CE2 B:PHE140 4.2 23.9 1.0
CA B:SER48 4.6 16.9 1.0
CG B:LEU141 4.6 19.6 1.0
CB B:HIS67 4.7 17.0 1.0
F4 B:PFB404 4.7 24.1 1.0
F2 B:PFB404 4.8 21.6 1.0
C B:SER48 4.8 18.2 1.0
CD1 B:PHE93 4.8 16.2 1.0
CE1 B:PHE93 4.9 16.9 1.0
CD1 B:LEU57 4.9 30.9 1.0

Reference:

K.K.Shanmuganatham, R.S.Wallace, A.T.Lee, B.V.Plapp. Contribution of Buried Distal Amino Acid Residues in Horse Liver Alcohol Dehydrogenase to Structure and Catalysis. Protein Sci. 2017.
ISSN: ESSN 1469-896X
PubMed: 29271062
DOI: 10.1002/PRO.3370
Page generated: Sun Dec 13 12:20:08 2020

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