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Fluorine in PDB 6owm: Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

Enzymatic activity of Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

All present enzymatic activity of Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 6owm 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) 19.62 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.470, 51.440, 92.560, 92.09, 102.95, 110.25
R / Rfree (%) 12.4 / 14.1

Other elements in 6owm:

The structure of Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol (pdb code 6owm). 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 F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 6owm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 6owm

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Fluorine binding site 1 out of 10 in the Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:14.7
occ:1.00
 F2 A:PFB404 0.0 14.7 1.0
C2 A:PFB404 1.3 12.9 1.0
C3 A:PFB404 2.3 13.7 1.0
C1 A:PFB404 2.3 13.3 1.0
F3 A:PFB404 2.7 15.1 1.0
C7N A:NAJ403 2.9 9.3 1.0
C7 A:PFB404 2.9 12.7 1.0
C3N A:NAJ403 2.9 9.5 1.0
O7N A:NAJ403 3.1 10.1 1.0
C2N A:NAJ403 3.3 9.0 1.0
N7N A:NAJ403 3.5 10.2 1.0
C4 A:PFB404 3.6 14.0 1.0
C6 A:PFB404 3.6 14.0 1.0
CH2 A:TRP93 3.6 11.4 1.0
C4N A:NAJ403 3.6 11.4 1.0
CD1 A:ILE318 3.7 16.0 1.0
CG2 A:VAL294 3.7 11.9 0.6
CG2 A:VAL294 3.8 12.5 0.4
O1 A:PFB404 3.8 11.8 1.0
CZ3 A:TRP93 4.0 10.7 1.0
C5 A:PFB404 4.1 13.8 1.0
N1N A:NAJ403 4.2 9.2 1.0
OG A:SER48 4.5 11.5 1.0
C5N A:NAJ403 4.5 10.6 1.0
CZ2 A:TRP93 4.5 11.3 1.0
F4 A:PFB404 4.6 18.4 1.0
F6 A:PFB404 4.7 14.8 1.0
CD1 A:LEU116 4.7 20.4 0.7
C6N A:NAJ403 4.8 9.5 1.0
CD2 B:LEU309 4.8 15.1 1.0
CD2 A:LEU116 5.0 17.2 0.3

Fluorine binding site 2 out of 10 in 6owm

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Fluorine binding site 2 out of 10 in the Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:15.1
occ:1.00
 F3 A:PFB404 0.0 15.1 1.0
C3 A:PFB404 1.3 13.7 1.0
C4 A:PFB404 2.3 14.0 1.0
C2 A:PFB404 2.4 12.9 1.0
F2 A:PFB404 2.7 14.7 1.0
F4 A:PFB404 2.7 18.4 1.0
CG2 A:VAL294 3.4 12.5 0.4
CD1 A:LEU116 3.4 20.4 0.7
CG2 A:VAL294 3.5 11.9 0.6
CD1 A:ILE318 3.6 16.0 1.0
C5 A:PFB404 3.6 13.8 1.0
CD2 B:LEU309 3.6 15.1 1.0
C1 A:PFB404 3.7 13.3 1.0
CD2 A:LEU116 3.9 17.2 0.3
CD2 A:LEU116 4.1 23.4 0.7
C6 A:PFB404 4.1 14.0 1.0
CG A:LEU116 4.1 17.8 0.7
O A:HOH1027 4.4 28.9 1.0
CG1 A:VAL294 4.5 13.8 0.4
CB A:VAL294 4.6 12.3 0.4
CB A:VAL294 4.6 11.9 0.6
CG1 A:VAL294 4.7 12.6 0.6
F5 A:PFB404 4.7 16.6 1.0
CG B:LEU309 4.9 12.3 1.0
C7 A:PFB404 4.9 12.7 1.0
CE B:MET306 5.0 20.1 1.0

Fluorine binding site 3 out of 10 in 6owm

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Fluorine binding site 3 out of 10 in the Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:18.4
occ:1.00
 F4 A:PFB404 0.0 18.4 1.0
C4 A:PFB404 1.3 14.0 1.0
C5 A:PFB404 2.3 13.8 1.0
C3 A:PFB404 2.4 13.7 1.0
F5 A:PFB404 2.7 16.6 1.0
F3 A:PFB404 2.7 15.1 1.0
CD1 A:LEU57 3.1 17.3 0.2
CD2 A:LEU57 3.2 15.6 0.8
CG A:LEU116 3.4 17.8 0.7
CD1 A:LEU116 3.5 20.4 0.7
CD2 A:LEU57 3.5 17.9 0.2
C2 A:PFB404 3.6 12.9 1.0
C6 A:PFB404 3.6 14.0 1.0
CD1 A:LEU57 3.7 15.5 0.8
CD2 A:LEU116 3.8 23.4 0.7
O A:HOH1027 3.8 28.9 1.0
CG A:LEU57 3.9 16.5 0.2
CD2 A:LEU116 4.0 17.2 0.3
CG A:LEU57 4.1 14.6 0.8
C1 A:PFB404 4.1 13.3 1.0
CG A:LEU116 4.3 14.6 0.3
F2 A:PFB404 4.6 14.7 1.0
F6 A:PFB404 4.7 14.8 1.0
CG2 A:VAL294 4.8 11.9 0.6
CG1 A:VAL294 4.8 13.8 0.4
CB A:LEU116 4.8 15.1 0.3
CB A:LEU116 4.8 17.4 0.7
CG2 A:VAL294 4.8 12.5 0.4
CG1 A:VAL294 4.9 12.6 0.6
CD2 A:LEU141 5.0 17.1 1.0

Fluorine binding site 4 out of 10 in 6owm

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Fluorine binding site 4 out of 10 in the Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:16.6
occ:1.00
 F5 A:PFB404 0.0 16.6 1.0
C5 A:PFB404 1.3 13.8 1.0
C4 A:PFB404 2.3 14.0 1.0
C6 A:PFB404 2.4 14.0 1.0
CD2 A:LEU57 2.7 17.9 0.2
F6 A:PFB404 2.7 14.8 1.0
F4 A:PFB404 2.7 18.4 1.0
CD1 A:LEU57 3.2 15.5 0.8
CZ A:PHE140 3.3 13.5 1.0
CD1 A:LEU141 3.4 14.1 1.0
C3 A:PFB404 3.6 13.7 1.0
C1 A:PFB404 3.6 13.3 1.0
CE1 A:PHE140 3.7 13.4 1.0
CD2 A:LEU141 3.9 17.1 1.0
CG A:LEU57 4.0 16.5 0.2
CG A:LEU141 4.0 14.0 1.0
C2 A:PFB404 4.1 12.9 1.0
CD1 A:LEU57 4.2 17.3 0.2
CE2 A:PHE140 4.3 14.2 1.0
CG A:LEU57 4.3 14.6 0.8
CD2 A:LEU57 4.3 15.6 0.8
CB A:SER48 4.5 10.8 1.0
F3 A:PFB404 4.7 15.1 1.0
CD1 A:LEU116 4.8 20.4 0.7
C7 A:PFB404 4.9 12.7 1.0
O A:HOH671 4.9 27.2 1.0
CD1 A:PHE140 5.0 12.7 1.0

Fluorine binding site 5 out of 10 in 6owm

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Fluorine binding site 5 out of 10 in the Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:14.8
occ:1.00
 F6 A:PFB404 0.0 14.8 1.0
C6 A:PFB404 1.3 14.0 1.0
C5 A:PFB404 2.3 13.8 1.0
C1 A:PFB404 2.4 13.3 1.0
F5 A:PFB404 2.7 16.6 1.0
C7 A:PFB404 2.8 12.7 1.0
O1 A:PFB404 3.1 11.8 1.0
CB A:SER48 3.2 10.8 1.0
CD1 A:LEU141 3.3 14.1 1.0
NE2 A:HIS67 3.3 11.7 1.0
CE1 A:HIS67 3.4 10.8 1.0
CD2 A:HIS67 3.5 10.9 1.0
C4 A:PFB404 3.6 14.0 1.0
C2 A:PFB404 3.6 12.9 1.0
OG A:SER48 3.7 11.5 1.0
ND1 A:HIS67 3.7 10.8 1.0
CG A:HIS67 3.8 10.2 1.0
CZ A:PHE140 4.0 13.5 1.0
C3 A:PFB404 4.1 13.7 1.0
ZN A:ZN401 4.1 10.3 0.8
CE2 A:PHE140 4.2 14.2 1.0
CA A:SER48 4.5 11.1 1.0
CG A:LEU141 4.6 14.0 1.0
CE3 A:TRP93 4.7 10.1 1.0
F4 A:PFB404 4.7 18.4 1.0
F2 A:PFB404 4.7 14.7 1.0
CB A:HIS67 4.8 10.2 1.0
CD1 A:LEU57 4.8 15.5 0.8
C A:SER48 4.8 11.7 1.0
CD2 A:LEU57 4.8 17.9 0.2
CZ3 A:TRP93 4.8 10.7 1.0
CD2 A:TRP93 4.8 9.8 1.0

Fluorine binding site 6 out of 10 in 6owm

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Fluorine binding site 6 out of 10 in the Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:16.4
occ:1.00
 F2 B:PFB404 0.0 16.4 1.0
C2 B:PFB404 1.3 14.4 1.0
C3 B:PFB404 2.3 14.9 1.0
C1 B:PFB404 2.4 14.4 1.0
F3 B:PFB404 2.6 16.4 1.0
C7N B:NAJ403 2.9 10.8 1.0
C7 B:PFB404 2.9 13.7 1.0
C3N B:NAJ403 3.0 10.8 1.0
O7N B:NAJ403 3.1 11.8 1.0
C2N B:NAJ403 3.3 10.8 1.0
N7N B:NAJ403 3.5 11.5 1.0
CG2 B:VAL294 3.5 14.0 0.5
C4 B:PFB404 3.6 16.5 1.0
C6 B:PFB404 3.6 14.1 1.0
CH2 B:TRP93 3.7 12.3 1.0
C4N B:NAJ403 3.7 12.2 1.0
CD1 B:ILE318 3.8 18.9 1.0
O1 B:PFB404 3.8 13.8 1.0
CG2 B:VAL294 4.0 12.3 0.5
CZ3 B:TRP93 4.1 12.1 1.0
C5 B:PFB404 4.1 15.1 1.0
N1N B:NAJ403 4.2 10.9 1.0
OG B:SER48 4.4 12.5 1.0
C5N B:NAJ403 4.6 12.1 1.0
CZ2 B:TRP93 4.6 12.7 1.0
F4 B:PFB404 4.6 19.8 1.0
F6 B:PFB404 4.7 15.4 1.0
CD1 B:LEU116 4.8 17.9 0.5
C6N B:NAJ403 4.8 11.2 1.0
CD2 A:LEU309 4.9 15.0 0.7
CD2 B:LEU116 4.9 22.1 0.6

Fluorine binding site 7 out of 10 in 6owm

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Fluorine binding site 7 out of 10 in the Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:16.4
occ:1.00
 F3 B:PFB404 0.0 16.4 1.0
C3 B:PFB404 1.3 14.9 1.0
C4 B:PFB404 2.3 16.5 1.0
C2 B:PFB404 2.3 14.4 1.0
F2 B:PFB404 2.6 16.4 1.0
F4 B:PFB404 2.7 19.8 1.0
CG2 B:VAL294 3.3 14.0 0.5
CD1 B:LEU116 3.5 17.9 0.5
CG2 B:VAL294 3.5 12.3 0.5
C5 B:PFB404 3.6 15.1 1.0
C1 B:PFB404 3.6 14.4 1.0
CD1 B:ILE318 3.6 18.9 1.0
CD2 A:LEU309 3.7 15.0 0.7
CD2 B:LEU116 3.7 22.1 0.6
C6 B:PFB404 4.1 14.1 1.0
CG B:LEU116 4.2 16.0 0.5
CG1 B:VAL294 4.2 13.5 0.5
CD2 B:LEU116 4.3 18.1 0.5
CB B:VAL294 4.4 13.0 0.5
F5 B:PFB404 4.7 17.4 1.0
CB B:VAL294 4.8 11.3 0.5
CG1 B:VAL294 4.8 11.7 0.5
CG A:LEU309 4.9 12.3 0.7
C7 B:PFB404 4.9 13.7 1.0
CG B:LEU116 5.0 21.5 0.6

Fluorine binding site 8 out of 10 in 6owm

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Fluorine binding site 8 out of 10 in the Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:19.8
occ:1.00
 F4 B:PFB404 0.0 19.8 1.0
C4 B:PFB404 1.3 16.5 1.0
C3 B:PFB404 2.4 14.9 1.0
C5 B:PFB404 2.4 15.1 1.0
F3 B:PFB404 2.7 16.4 1.0
F5 B:PFB404 2.7 17.4 1.0
CD2 B:LEU57 3.3 18.7 1.0
CG B:LEU116 3.5 16.0 0.5
CD1 B:LEU116 3.6 17.9 0.5
C2 B:PFB404 3.6 14.4 1.0
C6 B:PFB404 3.6 14.1 1.0
CD1 B:LEU57 3.6 21.8 1.0
CD2 B:LEU116 3.7 22.1 0.6
CD2 B:LEU116 3.9 18.1 0.5
CG B:LEU57 4.1 19.7 1.0
C1 B:PFB404 4.1 14.4 1.0
CG B:LEU116 4.1 21.5 0.6
CG1 B:VAL294 4.6 13.5 0.5
F2 B:PFB404 4.6 16.4 1.0
F6 B:PFB404 4.7 15.4 1.0
CB B:LEU116 4.8 18.7 0.6
CG2 B:VAL294 4.8 14.0 0.5
CB B:LEU116 4.8 16.0 0.5
CG2 B:VAL294 4.9 12.3 0.5

Fluorine binding site 9 out of 10 in 6owm

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Fluorine binding site 9 out of 10 in the Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:17.4
occ:1.00
 F5 B:PFB404 0.0 17.4 1.0
C5 B:PFB404 1.3 15.1 1.0
C4 B:PFB404 2.3 16.5 1.0
C6 B:PFB404 2.3 14.1 1.0
F6 B:PFB404 2.7 15.4 1.0
F4 B:PFB404 2.7 19.8 1.0
CD1 B:LEU57 3.2 21.8 1.0
CZ B:PHE140 3.3 15.3 1.0
CD1 B:LEU141 3.4 16.4 1.0
C3 B:PFB404 3.6 14.9 1.0
C1 B:PFB404 3.6 14.4 1.0
CE1 B:PHE140 3.8 15.0 1.0
CD2 B:LEU141 3.9 20.5 1.0
C2 B:PFB404 4.1 14.4 1.0
CG B:LEU141 4.1 15.7 1.0
CE2 B:PHE140 4.3 15.4 1.0
CG B:LEU57 4.4 19.7 1.0
CB B:SER48 4.5 12.3 1.0
CD2 B:LEU57 4.5 18.7 1.0
F3 B:PFB404 4.7 16.4 1.0
CD2 B:LEU116 4.8 22.1 0.6
C7 B:PFB404 4.9 13.7 1.0
CG B:LEU116 4.9 21.5 0.6
CD1 B:LEU116 5.0 17.9 0.5
O B:SER48 5.0 13.9 1.0

Fluorine binding site 10 out of 10 in 6owm

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Fluorine binding site 10 out of 10 in the Horse Liver F93W 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 Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:15.4
occ:1.00
 F6 B:PFB404 0.0 15.4 1.0
C6 B:PFB404 1.3 14.1 1.0
C5 B:PFB404 2.3 15.1 1.0
C1 B:PFB404 2.4 14.4 1.0
F5 B:PFB404 2.7 17.4 1.0
C7 B:PFB404 2.8 13.7 1.0
O1 B:PFB404 3.2 13.8 1.0
CB B:SER48 3.2 12.3 1.0
CD1 B:LEU141 3.3 16.4 1.0
NE2 B:HIS67 3.3 13.4 1.0
CE1 B:HIS67 3.4 12.5 1.0
CD2 B:HIS67 3.5 11.8 1.0
C4 B:PFB404 3.6 16.5 1.0
C2 B:PFB404 3.6 14.4 1.0
ND1 B:HIS67 3.7 12.1 1.0
OG B:SER48 3.8 12.5 1.0
CG B:HIS67 3.8 11.4 1.0
CZ B:PHE140 4.1 15.3 1.0
C3 B:PFB404 4.1 14.9 1.0
ZN B:ZN401 4.1 12.6 0.9
CE2 B:PHE140 4.3 15.4 1.0
CA B:SER48 4.6 13.1 1.0
CE3 B:TRP93 4.6 11.4 1.0
CG B:LEU141 4.7 15.7 1.0
F4 B:PFB404 4.7 19.8 1.0
F2 B:PFB404 4.7 16.4 1.0
CB B:HIS67 4.7 11.8 1.0
C B:SER48 4.7 12.7 1.0
CD2 B:TRP93 4.8 11.2 1.0
CZ3 B:TRP93 4.8 12.1 1.0
CD1 B:LEU57 4.9 21.8 1.0
O B:SER48 5.0 13.9 1.0

Reference:

B.V.Plapp, K.Kim. Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on Structure But Significantly Affect Catalysis of Hydrogen Transfer. To Be Published.
Page generated: Thu Aug 1 23:58:16 2024

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