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Fluorine in PDB 5kcp: Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

Enzymatic activity of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

All present enzymatic activity of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 5kcp 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) 19.40 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.440, 51.590, 92.560, 91.87, 103.06, 110.33
R / Rfree (%) 11.8 / 13.8

Other elements in 5kcp:

The structure of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Fluorine atom in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol (pdb code 5kcp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 20 binding sites of Fluorine where determined in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 5kcp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 20 in 5kcp

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Fluorine binding site 1 out of 20 in the Horse Liver S48T 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 S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:16.6
occ:1.00
 F2 A:PFB378 0.0 16.6 1.0
C2 A:PFB378 1.3 13.7 1.0
C3 A:PFB378 2.3 14.4 1.0
C1 A:PFB378 2.4 14.4 1.0
F3 A:PFB378 2.7 16.2 1.0
C7N A:NAJ377 2.8 9.5 1.0
C3N A:NAJ377 2.9 9.7 1.0
C7 A:PFB378 2.9 14.1 1.0
O7N A:NAJ377 3.0 10.9 1.0
C2N A:NAJ377 3.2 8.9 1.0
N7N A:NAJ377 3.3 9.6 1.0
C4 A:PFB378 3.6 14.0 1.0
C6 A:PFB378 3.6 16.1 1.0
CG2 A:VAL294 3.6 12.3 1.0
C4N A:NAJ377 3.7 11.2 1.0
O1 A:PFB378 3.8 12.8 1.0
CD1 A:ILE318 3.8 16.2 1.0
C5 A:PFB378 4.1 14.1 1.0
N1N A:NAJ377 4.1 9.3 1.0
OG1 A:THR48 4.5 11.5 1.0
C5N A:NAJ377 4.6 10.5 1.0
F4 A:PFB378 4.7 17.2 1.0
F6 A:PFB378 4.7 18.4 1.0
C6N A:NAJ377 4.7 9.8 1.0
CE1 A:PHE93 4.7 11.2 1.0
CD2 B:LEU309 4.8 16.1 1.0
CG2 A:ILE318 4.8 11.5 1.0
CZ A:PHE93 4.9 11.2 1.0
O A:VAL292 5.0 9.6 1.0
CD2 A:LEU116 5.0 14.9 1.0

Fluorine binding site 2 out of 20 in 5kcp

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Fluorine binding site 2 out of 20 in the Horse Liver S48T 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 S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:16.2
occ:1.00
 F3 A:PFB378 0.0 16.2 1.0
C3 A:PFB378 1.3 14.4 1.0
C4 A:PFB378 2.3 14.0 1.0
C2 A:PFB378 2.4 13.7 1.0
F2 A:PFB378 2.7 16.6 1.0
F4 A:PFB378 2.7 17.2 1.0
CG2 A:VAL294 3.4 12.3 1.0
CD1 A:ILE318 3.4 16.2 1.0
CD2 B:LEU309 3.6 16.1 1.0
C5 A:PFB378 3.6 14.1 1.0
C1 A:PFB378 3.6 14.4 1.0
CD2 A:LEU116 4.0 14.9 1.0
C6 A:PFB378 4.1 16.1 1.0
O A:HOH681 4.5 28.9 1.0
CB A:VAL294 4.6 11.6 1.0
CG1 A:VAL294 4.7 13.0 1.0
F5 A:PFB378 4.7 18.6 1.0
CG B:LEU309 4.7 13.1 1.0
CG1 A:ILE318 4.8 13.0 1.0
C7 A:PFB378 4.9 14.1 1.0
CG A:LEU116 5.0 13.9 1.0

Fluorine binding site 3 out of 20 in 5kcp

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Fluorine binding site 3 out of 20 in the Horse Liver S48T 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 S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:17.2
occ:1.00
 F4 A:PFB378 0.0 17.2 1.0
C4 A:PFB378 1.3 14.0 1.0
C5 A:PFB378 2.3 14.1 1.0
C3 A:PFB378 2.4 14.4 1.0
F3 A:PFB378 2.7 16.2 1.0
F5 A:PFB378 2.7 18.6 1.0
CD1 A:LEU57 3.5 18.5 1.0
C6 A:PFB378 3.6 16.1 1.0
C2 A:PFB378 3.6 13.7 1.0
CD2 A:LEU57 3.7 19.0 1.0
O A:HOH730 3.7 26.5 1.0
CD2 A:LEU116 3.8 14.9 1.0
CG A:LEU116 3.8 13.9 1.0
O A:HOH681 4.1 28.9 1.0
C1 A:PFB378 4.1 14.4 1.0
CB A:LEU116 4.2 13.3 1.0
CG A:LEU57 4.2 14.9 1.0
F2 A:PFB378 4.7 16.6 1.0
O A:LEU116 4.7 18.9 1.0
CA A:LEU116 4.7 13.3 1.0
F6 A:PFB378 4.7 18.4 1.0
CG2 A:THR48 4.8 15.9 1.0
CD2 A:LEU141 4.8 15.5 1.0
CG2 A:VAL294 5.0 12.3 1.0

Fluorine binding site 4 out of 20 in 5kcp

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Fluorine binding site 4 out of 20 in the Horse Liver S48T 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 S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:18.6
occ:1.00
 F5 A:PFB378 0.0 18.6 1.0
C5 A:PFB378 1.3 14.1 1.0
C6 A:PFB378 2.4 16.1 1.0
C4 A:PFB378 2.4 14.0 1.0
F4 A:PFB378 2.7 17.2 1.0
F6 A:PFB378 2.7 18.4 1.0
CD1 A:LEU141 3.1 13.7 1.0
CD2 A:LEU57 3.1 19.0 1.0
CD2 A:LEU141 3.2 15.5 1.0
CZ A:PHE140 3.4 12.6 1.0
C3 A:PFB378 3.6 14.4 1.0
CG A:LEU141 3.6 13.0 1.0
C1 A:PFB378 3.6 14.4 1.0
CG2 A:THR48 3.8 15.9 1.0
CE1 A:PHE140 3.9 12.7 1.0
C2 A:PFB378 4.1 13.7 1.0
CE2 A:PHE140 4.4 13.1 1.0
CG A:LEU57 4.4 14.9 1.0
CG A:LEU116 4.4 13.9 1.0
O A:HOH730 4.6 26.5 1.0
CD1 A:LEU57 4.6 18.5 1.0
CD2 A:LEU116 4.6 14.9 1.0
O A:HOH863 4.7 29.2 1.0
F3 A:PFB378 4.7 16.2 1.0
C7 A:PFB378 4.9 14.1 1.0
CB A:THR48 4.9 12.4 1.0

Fluorine binding site 5 out of 20 in 5kcp

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Fluorine binding site 5 out of 20 in the Horse Liver S48T 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 S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:18.4
occ:1.00
 F6 A:PFB378 0.0 18.4 1.0
C6 A:PFB378 1.3 16.1 1.0
C1 A:PFB378 2.3 14.4 1.0
C5 A:PFB378 2.4 14.1 1.0
F5 A:PFB378 2.7 18.6 1.0
C7 A:PFB378 2.7 14.1 1.0
CD1 A:LEU141 3.0 13.7 1.0
O1 A:PFB378 3.2 12.8 1.0
NE2 A:HIS67 3.3 11.9 1.0
CD2 A:HIS67 3.4 10.8 1.0
CG2 A:THR48 3.4 15.9 1.0
C2 A:PFB378 3.6 13.7 1.0
CE1 A:HIS67 3.6 11.3 1.0
C4 A:PFB378 3.6 14.0 1.0
CB A:THR48 3.6 12.4 1.0
CG A:HIS67 3.7 10.6 1.0
ND1 A:HIS67 3.8 10.6 1.0
C3 A:PFB378 4.1 14.4 1.0
OG1 A:THR48 4.1 11.5 1.0
ZN A:ZN375 4.1 12.9 1.0
CZ A:PHE140 4.2 12.6 1.0
CD1 A:PHE93 4.4 10.5 1.0
CE2 A:PHE140 4.4 13.1 1.0
CG A:LEU141 4.4 13.0 1.0
CE1 A:PHE93 4.5 11.2 1.0
CB A:HIS67 4.6 10.6 1.0
F2 A:PFB378 4.7 16.6 1.0
F4 A:PFB378 4.7 17.2 1.0
CG A:PHE93 4.7 10.2 1.0
CD2 A:LEU141 4.9 15.5 1.0
CZ A:PHE93 4.9 11.2 1.0

Fluorine binding site 6 out of 20 in 5kcp

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Fluorine binding site 6 out of 20 in the Horse Liver S48T 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 S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F379

b:31.5
occ:0.60
 F2 A:PFB379 0.0 31.5 0.6
C2 A:PFB379 1.3 26.3 0.6
C3 A:PFB379 2.3 24.9 0.6
C1 A:PFB379 2.3 25.7 0.6
F3 A:PFB379 2.7 30.6 0.6
C7 A:PFB379 2.8 28.8 0.6
O A:HOH914 3.3 26.6 1.0
O1 A:PFB379 3.5 37.0 0.6
C4 A:PFB379 3.6 20.6 0.6
C6 A:PFB379 3.6 21.1 0.6
C5 A:PFB379 4.0 18.4 0.6
F4 A:PFB379 4.7 25.6 0.6
F6 A:PFB379 4.7 25.4 0.6
O A:HOH829 4.9 21.7 1.0

Fluorine binding site 7 out of 20 in 5kcp

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Fluorine binding site 7 out of 20 in the Horse Liver S48T 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 S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F379

b:30.6
occ:0.60
 F3 A:PFB379 0.0 30.6 0.6
C3 A:PFB379 1.4 24.9 0.6
C2 A:PFB379 2.4 26.3 0.6
C4 A:PFB379 2.4 20.6 0.6
F2 A:PFB379 2.7 31.5 0.6
F4 A:PFB379 2.8 25.6 0.6
O A:HOH866 3.1 25.8 1.0
O A:HOH829 3.2 21.7 1.0
C5 A:PFB379 3.6 18.4 0.6
C1 A:PFB379 3.7 25.7 0.6
C6 A:PFB379 4.2 21.1 0.6
CG A:PRO136 4.2 20.0 1.0
NE2 A:HIS138 4.4 15.9 1.0
O A:HOH678 4.4 24.1 1.0
O A:HOH914 4.5 26.6 1.0
F5 A:PFB379 4.7 20.3 0.6
CE1 A:HIS138 4.7 15.2 1.0
C7 A:PFB379 4.9 28.8 0.6
CB A:PRO136 5.0 16.6 1.0

Fluorine binding site 8 out of 20 in 5kcp

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Fluorine binding site 8 out of 20 in the Horse Liver S48T 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 S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F379

b:25.6
occ:0.60
 F4 A:PFB379 0.0 25.6 0.6
C4 A:PFB379 1.4 20.6 0.6
C5 A:PFB379 2.3 18.4 0.6
C3 A:PFB379 2.4 24.9 0.6
F5 A:PFB379 2.6 20.3 0.6
F3 A:PFB379 2.8 30.6 0.6
O A:PRO136 3.1 15.9 1.0
NE2 A:HIS138 3.3 15.9 1.0
O A:HOH866 3.5 25.8 1.0
CD2 A:HIS138 3.5 13.5 1.0
O A:HOH678 3.5 24.1 1.0
C A:PRO136 3.6 14.5 1.0
C2 A:PFB379 3.6 26.3 0.6
C6 A:PFB379 3.6 21.1 0.6
CG A:PRO136 3.8 20.0 1.0
O A:HOH829 3.8 21.7 1.0
CE1 A:HIS138 3.8 15.2 1.0
CB A:PRO136 3.9 16.6 1.0
CG A:HIS138 4.2 12.5 1.0
C1 A:PFB379 4.2 25.7 0.6
N A:ILE137 4.2 13.9 1.0
N A:HIS138 4.3 12.3 1.0
ND1 A:HIS138 4.3 14.2 1.0
CA A:ILE137 4.3 13.8 1.0
CA A:PRO136 4.3 14.7 1.0
C A:ILE137 4.4 12.7 1.0
CD A:PRO62 4.6 13.9 1.0
F2 A:PFB379 4.7 31.5 0.6
F6 A:PFB379 4.7 25.4 0.6
CG A:PRO62 4.8 14.8 1.0
CD A:PRO136 4.9 17.9 1.0
O A:PRO62 5.0 12.6 1.0
CA A:HIS138 5.0 11.8 1.0

Fluorine binding site 9 out of 20 in 5kcp

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Fluorine binding site 9 out of 20 in the Horse Liver S48T 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 S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F379

b:20.3
occ:0.60
 F5 A:PFB379 0.0 20.3 0.6
C5 A:PFB379 1.3 18.4 0.6
C4 A:PFB379 2.3 20.6 0.6
C6 A:PFB379 2.4 21.1 0.6
F4 A:PFB379 2.6 25.6 0.6
F6 A:PFB379 2.8 25.4 0.6
C A:ILE137 3.1 12.7 1.0
N A:HIS138 3.1 12.3 1.0
O A:ILE137 3.2 13.3 1.0
CA A:HIS138 3.4 11.8 1.0
ND1 A:HIS138 3.4 14.2 1.0
CG A:HIS138 3.5 12.5 1.0
C3 A:PFB379 3.5 24.9 0.6
C1 A:PFB379 3.6 25.7 0.6
CE1 A:HIS138 3.6 15.2 1.0
N A:ILE137 3.6 13.9 1.0
CB A:SER128 3.7 16.2 1.0
CD2 A:HIS138 3.8 13.5 1.0
C A:PRO136 3.8 14.5 1.0
CA A:ILE137 3.8 13.8 1.0
NE2 A:HIS138 3.8 15.9 1.0
CB A:PRO136 3.9 16.6 1.0
C2 A:PFB379 4.0 26.3 0.6
O A:PRO136 4.0 15.9 1.0
CB A:HIS138 4.1 11.9 1.0
OG A:SER128 4.1 17.6 1.0
CA A:PRO136 4.4 14.7 1.0
O A:GLY121 4.6 13.6 1.0
CG A:PRO136 4.7 20.0 1.0
F3 A:PFB379 4.7 30.6 0.6
C A:HIS138 4.7 11.5 1.0
C7 A:PFB379 4.9 28.8 0.6

Fluorine binding site 10 out of 20 in 5kcp

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Fluorine binding site 10 out of 20 in the Horse Liver S48T 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 S48T Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F379

b:25.4
occ:0.60
 F6 A:PFB379 0.0 25.4 0.6
C6 A:PFB379 1.4 21.1 0.6
C1 A:PFB379 2.4 25.7 0.6
C5 A:PFB379 2.4 18.4 0.6
F5 A:PFB379 2.8 20.3 0.6
C7 A:PFB379 2.8 28.8 0.6
CB A:SER128 3.3 16.2 1.0
O1 A:PFB379 3.3 37.0 0.6
N A:SER128 3.5 14.7 1.0
CG2 A:THR122 3.6 16.6 1.0
C2 A:PFB379 3.6 26.3 0.6
C4 A:PFB379 3.7 20.6 0.6
C A:THR127 3.9 14.6 1.0
CA A:SER128 4.0 14.0 1.0
C3 A:PFB379 4.2 24.9 0.6
ND1 A:HIS138 4.2 14.2 1.0
O A:GLY121 4.3 13.6 1.0
CA A:THR127 4.3 15.6 1.0
CE1 A:HIS138 4.3 15.2 1.0
OG A:SER128 4.4 17.6 1.0
O A:GLY126 4.5 18.5 1.0
O A:THR127 4.5 16.1 1.0
CB A:THR122 4.5 15.8 1.0
O A:HOH914 4.6 26.6 1.0
F2 A:PFB379 4.7 31.5 0.6
F4 A:PFB379 4.7 25.6 0.6
CA A:THR122 4.8 13.6 1.0
O A:ILE137 5.0 13.3 1.0

Reference:

K.Kim, B.V.Plapp. Inversion of Substrate Stereoselectivity of Horse Liver Alcohol Dehydrogenase By Substitutions of Ser-48 and Phe-93. Chem. Biol. Interact. V. 276 77 2017.
ISSN: ISSN 1872-7786
PubMed: 28025168
DOI: 10.1016/J.CBI.2016.12.016
Page generated: Thu Aug 1 10:59:33 2024

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