Atomistry » Fluorine » PDB 5jwc-5knj » 5kjc
Atomistry »
  Fluorine »
    PDB 5jwc-5knj »
      5kjc »

Fluorine in PDB 5kjc: V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol

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

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

Protein crystallography data

The structure of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol, PDB code: 5kjc 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 (°) 44.230, 51.250, 92.550, 92.02, 103.01, 109.88
R / Rfree (%) 12.9 / 16.8

Other elements in 5kjc:

The structure of V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol (pdb code 5kjc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol, PDB code: 5kjc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 5kjc

Go back to Fluorine Binding Sites List in 5kjc
Fluorine binding site 1 out of 10 in the V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:20.1
occ:0.80
 F2 A:PFB378 0.0 20.1 0.8
C2 A:PFB378 1.3 17.8 0.8
C3 A:PFB378 2.3 19.3 0.8
C1 A:PFB378 2.4 18.8 0.8
F3 A:PFB378 2.7 20.6 0.8
C7N A:NAJ377 2.8 10.5 1.0
C3N A:NAJ377 2.9 11.3 1.0
C7 A:PFB378 2.9 21.5 0.8
O7N A:NAJ377 3.0 11.3 1.0
C2N A:NAJ377 3.4 10.6 1.0
N7N A:NAJ377 3.4 10.9 1.0
C4 A:PFB378 3.5 21.8 0.8
C6 A:PFB378 3.6 20.9 0.8
C4N A:NAJ377 3.6 14.1 1.0
CD1 A:ILE318 3.8 17.8 1.0
CG2 A:VAL294 3.8 16.8 1.0
O1 A:PFB378 3.9 15.8 0.8
C5 A:PFB378 4.0 21.1 0.8
N1N A:NAJ377 4.3 10.6 1.0
CE1 A:PHE93 4.5 12.4 1.0
CG2 A:ILE318 4.6 13.0 1.0
F4 A:PFB378 4.6 26.3 0.8
OG A:SER48 4.6 14.4 1.0
C5N A:NAJ377 4.7 12.8 1.0
F6 A:PFB378 4.7 20.5 0.8
CD2 A:LEU116 4.7 24.9 1.0
CZ A:PHE93 4.8 12.4 1.0
CD2 B:LEU309 4.8 15.5 0.6
C6N A:NAJ377 4.9 11.7 1.0
CG1 A:ILE318 5.0 13.3 1.0

Fluorine binding site 2 out of 10 in 5kjc

Go back to Fluorine Binding Sites List in 5kjc
Fluorine binding site 2 out of 10 in the V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:20.6
occ:0.80
 F3 A:PFB378 0.0 20.6 0.8
C3 A:PFB378 1.3 19.3 0.8
C4 A:PFB378 2.3 21.8 0.8
C2 A:PFB378 2.4 17.8 0.8
F4 A:PFB378 2.6 26.3 0.8
F2 A:PFB378 2.7 20.1 0.8
C5 A:PFB378 3.5 21.1 0.8
CG2 A:VAL294 3.6 16.8 1.0
CD1 A:ILE318 3.6 17.8 1.0
C1 A:PFB378 3.6 18.8 0.8
CD2 B:LEU309 3.7 15.5 0.6
CD2 A:LEU116 3.8 24.9 1.0
O A:HOH681 4.0 40.1 1.0
C6 A:PFB378 4.0 20.9 0.8
F5 A:PFB378 4.6 21.1 0.8
CG1 A:VAL294 4.7 17.2 1.0
CB A:VAL294 4.7 14.4 1.0
CG A:LEU116 4.8 20.4 1.0
CG B:LEU309 4.9 13.2 0.6
C7 A:PFB378 4.9 21.5 0.8
CG1 A:ILE318 4.9 13.3 1.0
CE B:MET306 5.0 29.8 1.0
CD2 A:LEU57 5.0 21.9 0.6

Fluorine binding site 3 out of 10 in 5kjc

Go back to Fluorine Binding Sites List in 5kjc
Fluorine binding site 3 out of 10 in the V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:26.3
occ:0.80
 F4 A:PFB378 0.0 26.3 0.8
C4 A:PFB378 1.3 21.8 0.8
C3 A:PFB378 2.3 19.3 0.8
C5 A:PFB378 2.4 21.1 0.8
F3 A:PFB378 2.6 20.6 0.8
F5 A:PFB378 2.8 21.1 0.8
CD1 A:LEU57 3.1 19.8 0.4
CD2 A:LEU57 3.3 21.9 0.6
C2 A:PFB378 3.6 17.8 0.8
O A:HOH681 3.6 40.1 1.0
C6 A:PFB378 3.6 20.9 0.8
CD2 A:LEU57 3.7 17.5 0.4
CD1 A:LEU57 3.8 17.5 0.6
CG A:LEU57 4.0 15.9 0.4
CD2 A:LEU116 4.0 24.9 1.0
O A:HOH682 4.0 54.2 1.0
C1 A:PFB378 4.1 18.8 0.8
CG A:LEU57 4.1 20.2 0.6
CG A:LEU116 4.2 20.4 1.0
CB A:LEU116 4.6 19.6 1.0
F2 A:PFB378 4.6 20.1 0.8
F6 A:PFB378 4.7 20.5 0.8
O A:LEU116 4.9 25.0 1.0
CG2 A:VAL294 4.9 16.8 1.0
CG1 A:VAL294 4.9 17.2 1.0
CD2 A:LEU141 4.9 18.3 1.0

Fluorine binding site 4 out of 10 in 5kjc

Go back to Fluorine Binding Sites List in 5kjc
Fluorine binding site 4 out of 10 in the V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:21.1
occ:0.80
 F5 A:PFB378 0.0 21.1 0.8
C5 A:PFB378 1.4 21.1 0.8
C6 A:PFB378 2.3 20.9 0.8
C4 A:PFB378 2.3 21.8 0.8
F6 A:PFB378 2.7 20.5 0.8
CD2 A:LEU57 2.7 17.5 0.4
F4 A:PFB378 2.8 26.3 0.8
CD1 A:LEU57 3.1 17.5 0.6
CD1 A:LEU141 3.3 15.7 1.0
CZ A:PHE140 3.4 14.2 1.0
C3 A:PFB378 3.6 19.3 0.8
C1 A:PFB378 3.6 18.8 0.8
CD2 A:LEU141 3.6 18.3 1.0
CE1 A:PHE140 3.8 14.5 1.0
CG A:LEU141 3.9 15.2 1.0
CG A:LEU57 3.9 15.9 0.4
CD1 A:LEU57 4.0 19.8 0.4
C2 A:PFB378 4.0 17.8 0.8
CE2 A:PHE140 4.3 14.6 1.0
CG A:LEU57 4.4 20.2 0.6
CD2 A:LEU57 4.4 21.9 0.6
CB A:SER48 4.5 12.7 1.0
F3 A:PFB378 4.6 20.6 0.8
C7 A:PFB378 4.8 21.5 0.8
CG A:LEU116 4.9 20.4 1.0
OG A:SER48 5.0 14.4 1.0

Fluorine binding site 5 out of 10 in 5kjc

Go back to Fluorine Binding Sites List in 5kjc
Fluorine binding site 5 out of 10 in the V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:20.5
occ:0.80
 F6 A:PFB378 0.0 20.5 0.8
C6 A:PFB378 1.4 20.9 0.8
C1 A:PFB378 2.3 18.8 0.8
C5 A:PFB378 2.4 21.1 0.8
F5 A:PFB378 2.7 21.1 0.8
C7 A:PFB378 2.7 21.5 0.8
O1 A:PFB378 3.1 15.8 0.8
CD1 A:LEU141 3.2 15.7 1.0
CB A:SER48 3.2 12.7 1.0
NE2 A:HIS67 3.3 14.0 1.0
CE1 A:HIS67 3.4 12.7 1.0
CD2 A:HIS67 3.4 13.8 1.0
C2 A:PFB378 3.6 17.8 0.8
C4 A:PFB378 3.6 21.8 0.8
OG A:SER48 3.7 14.4 1.0
ND1 A:HIS67 3.7 12.3 1.0
CG A:HIS67 3.7 11.1 1.0
C3 A:PFB378 4.1 19.3 0.8
ZN A:ZN375 4.1 16.9 0.8
CZ A:PHE140 4.1 14.2 1.0
CE2 A:PHE140 4.3 14.6 1.0
CG A:LEU141 4.5 15.2 1.0
CA A:SER48 4.6 13.0 1.0
CB A:HIS67 4.7 11.2 1.0
CD1 A:LEU57 4.7 17.5 0.6
F2 A:PFB378 4.7 20.1 0.8
CD1 A:PHE93 4.7 10.7 1.0
CD2 A:LEU57 4.7 17.5 0.4
F4 A:PFB378 4.7 26.3 0.8
CE1 A:PHE93 4.8 12.4 1.0
C A:SER48 4.9 13.1 1.0
CG A:PHE93 5.0 10.6 1.0

Fluorine binding site 6 out of 10 in 5kjc

Go back to Fluorine Binding Sites List in 5kjc
Fluorine binding site 6 out of 10 in the V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:26.9
occ:1.00
 F2 B:PFB378 0.0 26.9 1.0
C2 B:PFB378 1.3 25.7 1.0
C3 B:PFB378 2.2 23.7 1.0
C1 B:PFB378 2.4 23.7 1.0
F3 B:PFB378 2.6 26.9 1.0
C7N B:NAJ377 2.9 13.9 1.0
C7 B:PFB378 2.9 25.8 1.0
C3N B:NAJ377 3.0 12.8 1.0
O7N B:NAJ377 3.0 13.4 1.0
C2N B:NAJ377 3.4 12.4 1.0
N7N B:NAJ377 3.5 12.5 1.0
C4 B:PFB378 3.5 28.9 1.0
C6 B:PFB378 3.6 25.1 1.0
C4N B:NAJ377 3.7 17.3 1.0
CD1 B:ILE318 3.8 21.1 1.0
O1 B:PFB378 3.8 20.4 1.0
CG2 B:VAL294 3.9 19.7 1.0
C5 B:PFB378 4.0 28.6 1.0
N1N B:NAJ377 4.3 12.9 1.0
CE1 B:PHE93 4.5 15.1 1.0
OG B:SER48 4.6 16.1 1.0
CG2 B:ILE318 4.6 13.8 1.0
F4 B:PFB378 4.6 30.6 1.0
CD2 B:LEU116 4.6 26.4 1.0
C5N B:NAJ377 4.7 15.1 1.0
F6 B:PFB378 4.7 25.7 1.0
CD2 A:LEU309 4.8 18.4 0.6
CZ B:PHE93 4.8 15.6 1.0
C6N B:NAJ377 4.9 15.3 1.0
CG1 B:ILE318 5.0 15.1 1.0

Fluorine binding site 7 out of 10 in 5kjc

Go back to Fluorine Binding Sites List in 5kjc
Fluorine binding site 7 out of 10 in the V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:26.9
occ:1.00
 F3 B:PFB378 0.0 26.9 1.0
C3 B:PFB378 1.3 23.7 1.0
C2 B:PFB378 2.3 25.7 1.0
C4 B:PFB378 2.3 28.9 1.0
F2 B:PFB378 2.6 26.9 1.0
F4 B:PFB378 2.7 30.6 1.0
CG2 B:VAL294 3.6 19.7 1.0
C5 B:PFB378 3.6 28.6 1.0
C1 B:PFB378 3.6 23.7 1.0
CD1 B:ILE318 3.6 21.1 1.0
CD2 A:LEU309 3.7 18.4 0.6
CD2 B:LEU116 3.8 26.4 1.0
C6 B:PFB378 4.1 25.1 1.0
CG1 B:VAL294 4.6 19.2 1.0
F5 B:PFB378 4.7 28.1 1.0
CB B:VAL294 4.8 16.5 1.0
CE A:MET306 4.8 51.9 1.0
CG A:LEU309 4.8 15.5 0.6
CG B:LEU116 4.9 25.1 1.0
C7 B:PFB378 4.9 25.8 1.0
CG1 B:ILE318 5.0 15.1 1.0

Fluorine binding site 8 out of 10 in 5kjc

Go back to Fluorine Binding Sites List in 5kjc
Fluorine binding site 8 out of 10 in the V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:30.6
occ:1.00
 F4 B:PFB378 0.0 30.6 1.0
C4 B:PFB378 1.3 28.9 1.0
C3 B:PFB378 2.3 23.7 1.0
C5 B:PFB378 2.4 28.6 1.0
F3 B:PFB378 2.7 26.9 1.0
F5 B:PFB378 2.8 28.1 1.0
CD2 B:LEU57 3.2 31.1 1.0
C2 B:PFB378 3.5 25.7 1.0
C6 B:PFB378 3.6 25.1 1.0
CD1 B:LEU57 3.6 32.0 1.0
O B:HOH776 3.7 47.6 1.0
CD2 B:LEU116 4.0 26.4 1.0
CG B:LEU57 4.0 28.6 1.0
C1 B:PFB378 4.1 23.7 1.0
CG B:LEU116 4.3 25.1 1.0
F2 B:PFB378 4.6 26.9 1.0
F6 B:PFB378 4.7 25.7 1.0
CB B:LEU116 4.7 24.0 1.0
CG1 B:VAL294 4.9 19.2 1.0
CG2 B:VAL294 4.9 19.7 1.0

Fluorine binding site 9 out of 10 in 5kjc

Go back to Fluorine Binding Sites List in 5kjc
Fluorine binding site 9 out of 10 in the V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:28.1
occ:1.00
 F5 B:PFB378 0.0 28.1 1.0
C5 B:PFB378 1.4 28.6 1.0
C6 B:PFB378 2.3 25.1 1.0
C4 B:PFB378 2.4 28.9 1.0
F6 B:PFB378 2.7 25.7 1.0
F4 B:PFB378 2.8 30.6 1.0
CD1 B:LEU57 3.0 32.0 1.0
CZ B:PHE140 3.3 19.7 1.0
CD1 B:LEU141 3.4 17.3 1.0
C1 B:PFB378 3.6 23.7 1.0
C3 B:PFB378 3.6 23.7 1.0
CD2 B:LEU141 3.8 19.9 1.0
CE1 B:PHE140 3.8 16.7 1.0
CG B:LEU141 4.0 16.2 1.0
C2 B:PFB378 4.1 25.7 1.0
CG B:LEU57 4.2 28.6 1.0
CE2 B:PHE140 4.3 19.6 1.0
CD2 B:LEU57 4.4 31.1 1.0
CB B:SER48 4.4 15.3 1.0
O B:HOH776 4.5 47.6 1.0
F3 B:PFB378 4.7 26.9 1.0
O B:HOH755 4.8 36.3 1.0
C7 B:PFB378 4.8 25.8 1.0
OG B:SER48 4.9 16.1 1.0
O B:SER48 5.0 16.6 1.0
CG B:LEU116 5.0 25.1 1.0

Fluorine binding site 10 out of 10 in 5kjc

Go back to Fluorine Binding Sites List in 5kjc
Fluorine binding site 10 out of 10 in the V222I 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 V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F378

b:25.7
occ:1.00
 F6 B:PFB378 0.0 25.7 1.0
C6 B:PFB378 1.4 25.1 1.0
C5 B:PFB378 2.4 28.6 1.0
C1 B:PFB378 2.4 23.7 1.0
F5 B:PFB378 2.7 28.1 1.0
C7 B:PFB378 2.8 25.8 1.0
O1 B:PFB378 3.2 20.4 1.0
CD1 B:LEU141 3.2 17.3 1.0
CB B:SER48 3.2 15.3 1.0
NE2 B:HIS67 3.3 16.0 1.0
CE1 B:HIS67 3.4 14.7 1.0
CD2 B:HIS67 3.4 16.3 1.0
C4 B:PFB378 3.6 28.9 1.0
C2 B:PFB378 3.6 25.7 1.0
ND1 B:HIS67 3.7 14.6 1.0
CG B:HIS67 3.7 14.0 1.0
OG B:SER48 3.7 16.1 1.0
ZN B:ZN375 4.1 20.7 0.9
C3 B:PFB378 4.1 23.7 1.0
CZ B:PHE140 4.1 19.7 1.0
CE2 B:PHE140 4.3 19.6 1.0
CG B:LEU141 4.6 16.2 1.0
CA B:SER48 4.6 16.1 1.0
CB B:HIS67 4.7 13.2 1.0
F4 B:PFB378 4.7 30.6 1.0
F2 B:PFB378 4.7 26.9 1.0
CD1 B:PHE93 4.8 14.2 1.0
C B:SER48 4.8 15.8 1.0
CD1 B:LEU57 4.8 32.0 1.0
CE1 B:PHE93 4.9 15.1 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 11:05:31 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy