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Zinc 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:

Fluorine (F) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol, PDB code: 5kjc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5kjc

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Zinc binding site 1 out of 4 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn375

b:16.9
occ:0.80
 O1 A:PFB378 1.9 15.8 0.8
NE2 A:HIS67 2.1 14.0 1.0
SG A:CYS174 2.3 15.4 1.0
SG A:CYS46 2.3 16.4 0.8
C7 A:PFB378 2.9 21.5 0.8
CD2 A:HIS67 3.1 13.8 1.0
CE1 A:HIS67 3.1 12.7 1.0
C5N A:NAJ377 3.3 12.8 1.0
CB A:CYS174 3.4 12.1 1.0
CB A:CYS46 3.4 14.8 0.8
CB A:CYS46 3.5 16.4 0.2
SG A:CYS46 3.7 18.2 0.2
C4N A:NAJ377 3.8 14.1 1.0
OG A:SER48 3.9 14.4 1.0
C6N A:NAJ377 3.9 11.7 1.0
F6 A:PFB378 4.1 20.5 0.8
CB A:SER48 4.1 12.7 1.0
ND1 A:HIS67 4.2 12.3 1.0
CG A:HIS67 4.2 11.1 1.0
C1 A:PFB378 4.2 18.8 0.8
C6 A:PFB378 4.6 20.9 0.8
NH2 A:ARG369 4.7 20.8 1.0
CA A:CYS174 4.8 10.6 1.0
CE2 A:PHE93 4.8 14.1 1.0
N A:SER48 4.9 12.4 1.0
N1N A:NAJ377 5.0 10.6 1.0
CA A:CYS46 5.0 15.4 1.0

Zinc binding site 2 out of 4 in 5kjc

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Zinc binding site 2 out of 4 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn376

b:12.5
occ:1.00
 SG A:CYS97 2.3 14.2 1.0
SG A:CYS100 2.3 13.3 1.0
SG A:CYS111 2.3 12.0 1.0
SG A:CYS103 2.4 12.0 1.0
CB A:CYS111 3.3 11.5 1.0
CB A:CYS103 3.4 13.0 1.0
CB A:CYS100 3.4 13.9 1.0
CB A:CYS97 3.4 13.8 1.0
N A:CYS97 3.5 11.7 1.0
CA A:CYS111 3.7 10.9 1.0
N A:CYS100 3.9 15.4 1.0
CA A:CYS97 3.9 13.4 1.0
N A:GLY98 3.9 13.6 1.0
N A:LEU112 4.0 11.7 1.0
N A:CYS103 4.2 12.5 1.0
CA A:CYS100 4.2 15.8 1.0
C A:CYS111 4.3 11.2 1.0
C A:CYS97 4.3 13.8 1.0
CA A:CYS103 4.4 11.7 1.0
N A:LYS99 4.5 16.2 1.0
C A:GLN96 4.6 11.6 1.0
N A:LYS113 4.8 11.8 1.0
C A:CYS100 4.9 14.2 1.0
CG A:LYS113 4.9 18.0 1.0
O A:CYS100 4.9 14.4 1.0
CA A:GLN96 4.9 11.7 1.0
CA A:GLY98 4.9 14.8 1.0
O A:HOH552 5.0 32.9 1.0

Zinc binding site 3 out of 4 in 5kjc

Go back to Zinc Binding Sites List in 5kjc
Zinc binding site 3 out of 4 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn375

b:20.7
occ:0.90
 O1 B:PFB378 1.9 20.4 1.0
NE2 B:HIS67 2.1 16.0 1.0
SG B:CYS174 2.3 18.2 1.0
SG B:CYS46 2.3 21.6 1.0
C7 B:PFB378 2.9 25.8 1.0
CE1 B:HIS67 3.0 14.7 1.0
CD2 B:HIS67 3.1 16.3 1.0
C5N B:NAJ377 3.3 15.1 1.0
CB B:CYS46 3.4 18.2 1.0
CB B:CYS174 3.4 15.2 1.0
C4N B:NAJ377 3.8 17.3 1.0
OG B:SER48 3.9 16.1 1.0
C6N B:NAJ377 3.9 15.3 1.0
CB B:SER48 4.0 15.3 1.0
F6 B:PFB378 4.1 25.7 1.0
ND1 B:HIS67 4.2 14.6 1.0
CG B:HIS67 4.2 14.0 1.0
C1 B:PFB378 4.2 23.7 1.0
NH2 B:ARG369 4.6 23.4 1.0
C6 B:PFB378 4.6 25.1 1.0
CA B:CYS174 4.8 13.6 1.0
CE2 B:PHE93 4.9 15.9 1.0
N B:SER48 4.9 15.1 1.0
CA B:CYS46 4.9 17.6 1.0
N1N B:NAJ377 5.0 12.9 1.0

Zinc binding site 4 out of 4 in 5kjc

Go back to Zinc Binding Sites List in 5kjc
Zinc binding site 4 out of 4 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn376

b:15.8
occ:1.00
 SG B:CYS111 2.3 15.2 1.0
SG B:CYS97 2.3 18.7 1.0
SG B:CYS100 2.3 16.3 1.0
SG B:CYS103 2.4 14.6 1.0
CB B:CYS111 3.3 13.6 1.0
CB B:CYS97 3.4 16.3 1.0
CB B:CYS103 3.4 14.8 1.0
CB B:CYS100 3.4 17.7 1.0
N B:CYS97 3.5 14.9 1.0
CA B:CYS111 3.7 12.8 1.0
N B:CYS100 3.9 19.5 1.0
CA B:CYS97 3.9 17.7 1.0
N B:GLY98 3.9 17.6 1.0
N B:LEU112 4.0 14.3 1.0
CA B:CYS100 4.2 18.9 1.0
N B:CYS103 4.2 14.8 1.0
C B:CYS111 4.3 13.9 1.0
C B:CYS97 4.3 18.5 1.0
CA B:CYS103 4.4 13.8 1.0
N B:LYS99 4.5 18.9 1.0
C B:GLN96 4.6 14.1 1.0
N B:LYS113 4.8 15.0 1.0
C B:CYS100 4.8 18.2 1.0
CG B:LYS113 4.9 19.4 1.0
CA B:GLN96 4.9 13.8 1.0
O B:CYS100 5.0 17.1 1.0
CA B:GLY98 5.0 19.3 1.0
O B:HOH482 5.0 39.7 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: Sun Oct 27 20:27:08 2024

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