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Zinc in PDB 5kjf: V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol

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

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

Protein crystallography data

The structure of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol, PDB code: 5kjf 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 (°) 44.200, 51.330, 92.530, 91.88, 103.06, 109.84
R / Rfree (%) 13.3 / 15.3

Other elements in 5kjf:

The structure of V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol also contains other interesting chemical elements:

Fluorine (F) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol (pdb code 5kjf). 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 Trifluoroethanol, PDB code: 5kjf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5kjf

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


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 Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:15.8
occ:0.80
 O A:ETF378 2.0 14.5 1.0
NE2 A:HIS67 2.1 15.3 1.0
SG A:CYS174 2.2 15.0 1.0
SG A:CYS46 2.4 16.3 0.8
C2 A:ETF378 3.0 16.7 0.8
CE1 A:HIS67 3.1 12.7 1.0
CD2 A:HIS67 3.1 14.9 1.0
C2 A:ETF378 3.2 15.6 0.2
C5N A:NAJ377 3.3 11.4 1.0
CB A:CYS174 3.4 12.3 1.0
CB A:CYS46 3.5 14.8 0.8
CB A:CYS46 3.5 15.5 0.2
SG A:CYS46 3.6 19.6 0.2
OG A:SER48 3.7 12.9 1.0
C4N A:NAJ377 3.8 11.1 1.0
CB A:SER48 4.0 12.2 1.0
C6N A:NAJ377 4.0 10.4 1.0
ND1 A:HIS67 4.2 12.1 1.0
F3 A:ETF378 4.2 18.5 0.2
CG A:HIS67 4.2 11.1 1.0
C1 A:ETF378 4.3 16.4 0.2
C1 A:ETF378 4.4 17.0 0.8
F3 A:ETF378 4.7 20.6 0.8
CA A:CYS174 4.7 10.7 1.0
NH2 A:ARG369 4.8 20.2 1.0
F1 A:ETF378 4.8 21.8 0.8
CE2 A:PHE93 4.8 12.9 1.0
N A:SER48 4.9 11.3 1.0
N1N A:NAJ377 5.0 10.0 1.0
CA A:CYS46 5.0 14.7 1.0
F1 A:ETF378 5.0 16.4 0.2

Zinc binding site 2 out of 4 in 5kjf

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


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 Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:12.8
occ:1.00
 SG A:CYS111 2.3 12.4 1.0
SG A:CYS97 2.3 14.3 1.0
SG A:CYS100 2.3 13.1 1.0
SG A:CYS103 2.3 12.4 1.0
CB A:CYS111 3.3 12.2 1.0
CB A:CYS103 3.4 12.5 1.0
CB A:CYS100 3.4 13.9 1.0
CB A:CYS97 3.4 15.0 1.0
N A:CYS97 3.5 12.2 1.0
CA A:CYS111 3.7 10.5 1.0
N A:CYS100 3.9 15.2 1.0
CA A:CYS97 3.9 13.7 1.0
N A:LEU112 4.0 11.9 1.0
N A:GLY98 4.0 13.8 1.0
N A:CYS103 4.2 12.8 1.0
CA A:CYS100 4.2 14.9 1.0
C A:CYS111 4.3 11.0 1.0
C A:CYS97 4.3 14.2 1.0
CA A:CYS103 4.4 11.9 1.0
N A:LYS99 4.5 15.9 1.0
C A:GLN96 4.6 12.0 1.0
C A:CYS100 4.9 14.9 1.0
N A:LYS113 4.9 12.9 1.0
CG A:LYS113 4.9 16.2 1.0
CA A:GLN96 4.9 11.5 1.0
O A:CYS100 4.9 14.5 1.0

Zinc binding site 3 out of 4 in 5kjf

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Zinc binding site 3 out of 4 in the V222I Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Trifluoroethanol


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 Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:20.0
occ:0.80
 O B:ETF378 2.0 19.4 1.0
NE2 B:HIS67 2.1 18.7 1.0
SG B:CYS174 2.3 18.6 1.0
SG B:CYS46 2.4 21.3 1.0
C2 B:ETF378 3.0 21.4 1.0
CE1 B:HIS67 3.1 16.1 1.0
CD2 B:HIS67 3.1 18.1 1.0
C5N B:NAJ377 3.3 14.3 1.0
CB B:CYS174 3.4 14.6 1.0
CB B:CYS46 3.4 18.8 1.0
OG B:SER48 3.7 16.1 1.0
C4N B:NAJ377 3.8 14.6 1.0
CB B:SER48 3.9 15.8 1.0
C6N B:NAJ377 4.0 13.6 1.0
ND1 B:HIS67 4.2 15.4 1.0
CG B:HIS67 4.2 14.3 1.0
C1 B:ETF378 4.4 23.5 1.0
F3 B:ETF378 4.7 29.5 1.0
NH2 B:ARG369 4.7 23.4 1.0
CA B:CYS174 4.8 13.5 1.0
F1 B:ETF378 4.8 29.8 1.0
CE2 B:PHE93 4.9 15.0 1.0
N B:SER48 4.9 14.7 1.0
CA B:CYS46 5.0 17.6 1.0
N1N B:NAJ377 5.0 12.8 1.0

Zinc binding site 4 out of 4 in 5kjf

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


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 Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:15.7
occ:1.00
 SG B:CYS111 2.3 15.3 1.0
SG B:CYS100 2.3 16.4 1.0
SG B:CYS97 2.3 18.1 1.0
SG B:CYS103 2.4 14.3 1.0
CB B:CYS111 3.3 14.4 1.0
CB B:CYS100 3.4 17.9 1.0
CB B:CYS103 3.4 14.8 1.0
CB B:CYS97 3.4 16.8 1.0
N B:CYS97 3.5 15.6 1.0
CA B:CYS111 3.7 13.4 1.0
N B:CYS100 3.9 17.6 1.0
CA B:CYS97 3.9 16.8 1.0
N B:LEU112 3.9 14.4 1.0
N B:GLY98 4.0 17.3 1.0
CA B:CYS100 4.2 18.0 1.0
N B:CYS103 4.2 13.7 1.0
C B:CYS111 4.2 14.1 1.0
C B:CYS97 4.3 17.6 1.0
CA B:CYS103 4.4 13.9 1.0
N B:LYS99 4.5 18.5 1.0
C B:GLN96 4.6 14.1 1.0
N B:LYS113 4.8 15.9 1.0
C B:CYS100 4.9 17.7 1.0
CG B:LYS113 4.9 20.1 1.0
CA B:GLN96 4.9 13.7 1.0
O B:CYS100 4.9 16.2 1.0
CA B:GLY98 5.0 17.8 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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