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Zinc in PDB 4dxh: Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol

Enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol, PDB code: 4dxh was solved by B.V.Plapp, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.12
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.250, 51.160, 92.530, 91.91, 103.02, 109.90
R / Rfree (%) 12.7 / 14.7

Other elements in 4dxh:

The structure of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol (pdb code 4dxh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol, PDB code: 4dxh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4dxh

Go back to Zinc Binding Sites List in 4dxh
Zinc binding site 1 out of 4 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:9.1
occ:1.00
 O A:ETF378 2.0 9.8 1.0
NE2 A:HIS67 2.0 9.2 1.0
SG A:CYS174 2.3 9.0 1.0
SG A:CYS46 2.4 8.7 1.0
C2 A:ETF378 2.9 9.9 1.0
CE1 A:HIS67 3.0 7.9 1.0
CD2 A:HIS67 3.1 9.0 1.0
CB A:CYS46 3.3 8.8 1.0
C5N A:NAJ377 3.3 7.9 1.0
CB A:CYS174 3.4 8.2 1.0
OG A:SER48 3.8 8.6 1.0
C4N A:NAJ377 3.9 8.3 1.0
C6N A:NAJ377 4.0 7.7 1.0
CB A:SER48 4.0 7.9 1.0
ND1 A:HIS67 4.2 8.4 1.0
CG A:HIS67 4.2 7.7 1.0
C1 A:ETF378 4.2 12.3 1.0
F3 A:ETF378 4.6 15.9 1.0
NH2 A:ARG369 4.6 9.4 1.0
CA A:CYS174 4.8 7.5 1.0
CA A:CYS46 4.8 8.6 1.0
F1 A:ETF378 4.8 16.0 1.0
N A:SER48 4.8 8.1 1.0
OE2 A:GLU68 4.9 10.6 1.0
CE2 A:PHE93 4.9 8.8 1.0
N1N A:NAJ377 4.9 7.3 1.0

Zinc binding site 2 out of 4 in 4dxh

Go back to Zinc Binding Sites List in 4dxh
Zinc binding site 2 out of 4 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:10.4
occ:1.00
 SG A:CYS111 2.3 10.1 1.0
SG A:CYS97 2.4 12.1 1.0
SG A:CYS100 2.4 10.8 1.0
SG A:CYS103 2.4 10.2 1.0
CB A:CYS111 3.3 9.5 1.0
CB A:CYS100 3.4 12.0 1.0
CB A:CYS97 3.4 12.4 1.0
CB A:CYS103 3.4 10.4 1.0
N A:CYS97 3.6 10.3 1.0
CA A:CYS111 3.7 9.3 1.0
N A:CYS100 3.9 13.1 1.0
CA A:CYS97 3.9 11.1 1.0
N A:GLY98 4.0 11.6 1.0
N A:LEU112 4.0 9.6 1.0
N A:CYS103 4.2 10.1 1.0
CA A:CYS100 4.2 13.0 1.0
C A:CYS97 4.3 11.9 1.0
C A:CYS111 4.3 9.2 1.0
CA A:CYS103 4.4 9.8 1.0
N A:LYS99 4.5 14.0 1.0
C A:GLN96 4.6 9.6 1.0
C A:CYS100 4.8 12.8 1.0
N A:LYS113 4.9 10.5 1.0
CG A:LYS113 4.9 14.6 1.0
O A:CYS100 4.9 11.8 1.0
CA A:GLN96 4.9 9.0 1.0
CA A:GLY98 5.0 13.2 1.0

Zinc binding site 3 out of 4 in 4dxh

Go back to Zinc Binding Sites List in 4dxh
Zinc binding site 3 out of 4 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:12.1
occ:1.00
 O B:ETF378 1.9 12.6 1.0
NE2 B:HIS67 2.0 12.8 1.0
SG B:CYS174 2.3 11.9 1.0
SG B:CYS46 2.3 11.7 1.0
C2 B:ETF378 2.9 13.0 1.0
CE1 B:HIS67 3.0 11.6 1.0
CD2 B:HIS67 3.0 12.0 1.0
CB B:CYS46 3.3 11.8 1.0
C5N B:NAJ377 3.3 10.6 1.0
CB B:CYS174 3.4 10.8 1.0
OG B:SER48 3.8 11.5 1.0
C4N B:NAJ377 3.9 10.5 1.0
CB B:SER48 4.0 11.1 1.0
C6N B:NAJ377 4.0 9.8 1.0
ND1 B:HIS67 4.2 11.5 1.0
CG B:HIS67 4.2 11.3 1.0
C1 B:ETF378 4.3 15.7 1.0
F3 B:ETF378 4.6 18.4 1.0
NH2 B:ARG369 4.6 12.5 1.0
CA B:CYS174 4.7 10.5 1.0
CA B:CYS46 4.8 11.7 1.0
F1 B:ETF378 4.8 19.0 1.0
N B:SER48 4.9 11.1 1.0
OE2 B:GLU68 4.9 13.2 1.0
CE2 B:PHE93 4.9 11.5 1.0
N1N B:NAJ377 4.9 9.9 1.0

Zinc binding site 4 out of 4 in 4dxh

Go back to Zinc Binding Sites List in 4dxh
Zinc binding site 4 out of 4 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2,2,2- Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:13.7
occ:1.00
 SG B:CYS111 2.3 13.2 1.0
SG B:CYS103 2.4 12.6 1.0
SG B:CYS100 2.4 14.3 1.0
SG B:CYS97 2.4 16.8 1.0
CB B:CYS111 3.3 13.1 1.0
CB B:CYS100 3.4 16.1 1.0
CB B:CYS103 3.4 12.7 1.0
CB B:CYS97 3.4 16.8 1.0
N B:CYS97 3.5 13.8 1.0
CA B:CYS111 3.8 11.7 1.0
N B:CYS100 3.9 16.2 1.0
CA B:CYS97 3.9 15.1 1.0
N B:LEU112 4.0 12.9 1.0
N B:GLY98 4.0 15.4 1.0
CA B:CYS100 4.2 16.6 1.0
N B:CYS103 4.2 11.8 1.0
C B:CYS111 4.3 12.1 1.0
C B:CYS97 4.3 16.0 1.0
CA B:CYS103 4.4 11.8 1.0
N B:LYS99 4.5 17.3 1.0
C B:GLN96 4.6 12.7 1.0
C B:CYS100 4.8 14.8 1.0
N B:LYS113 4.9 13.1 1.0
CG B:LYS113 4.9 18.8 1.0
CA B:GLN96 4.9 11.6 1.0
O B:CYS100 4.9 14.7 1.0
CA B:GLY98 5.0 17.1 1.0

Reference:

B.V.Plapp, S.Ramaswamy. Atomic-Resolution Structures of Horse Liver Alcohol Dehydrogenase with Nad(+) and Fluoroalcohols Define Strained Michaelis Complexes. Biochemistry V. 51 4035 2012.
ISSN: ISSN 0006-2960
PubMed: 22531044
DOI: 10.1021/BI300378N
Page generated: Sat Oct 26 21:42:40 2024

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