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Zinc in PDB 4nfs: V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,2, 2-Trifluoroethanol

Enzymatic activity of V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,2, 2-Trifluoroethanol

All present enzymatic activity of V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,2, 2-Trifluoroethanol:
1.1.1.1;

Protein crystallography data

The structure of V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,2, 2-Trifluoroethanol, PDB code: 4nfs 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) 19.58 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.280, 51.410, 92.530, 91.88, 103.09, 109.94
R / Rfree (%) 13.7 / 17.5

Other elements in 4nfs:

The structure of V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,2, 2-Trifluoroethanol (pdb code 4nfs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,2, 2-Trifluoroethanol, PDB code: 4nfs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4nfs

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Zinc binding site 1 out of 4 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,2, 2-Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:12.8
occ:0.60
 O A:ETF378 2.0 12.6 0.8
NE2 A:HIS67 2.2 17.1 1.0
SG A:CYS174 2.2 14.6 1.0
SG A:CYS46 2.3 12.5 0.6
O A:HOH995 2.9 18.2 0.5
C2 A:ETF378 3.0 14.4 0.8
CE1 A:HIS67 3.2 14.4 1.0
CD2 A:HIS67 3.2 14.6 1.0
CB A:CYS174 3.4 11.6 1.0
CB A:CYS46 3.5 16.0 0.8
C5N A:NAJ377 3.5 10.5 1.0
OG A:SER48 3.7 12.8 1.0
SG A:CYS46 3.8 23.2 0.4
C4N A:NAJ377 3.8 10.9 1.0
CB A:CYS46 3.8 14.9 0.2
CB A:SER48 3.9 11.9 1.0
C6N A:NAJ377 4.2 10.3 1.0
ND1 A:HIS67 4.3 11.5 1.0
O A:HOH994 4.3 16.7 0.6
CG A:HIS67 4.3 10.8 1.0
C1 A:ETF378 4.3 17.0 0.8
F3 A:ETF378 4.6 22.6 0.8
CA A:CYS174 4.7 9.4 1.0
CE2 A:PHE93 4.7 11.5 1.0
F1 A:ETF378 4.8 22.0 0.8
N A:SER48 4.9 10.3 1.0
CZ A:PHE93 4.9 11.7 1.0
NH2 A:ARG369 5.0 13.3 0.5

Zinc binding site 2 out of 4 in 4nfs

Go back to Zinc Binding Sites List in 4nfs
Zinc binding site 2 out of 4 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,2, 2-Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:11.7
occ:1.00
 SG A:CYS111 2.3 11.2 1.0
SG A:CYS100 2.3 12.5 1.0
SG A:CYS97 2.3 13.1 1.0
SG A:CYS103 2.4 11.5 1.0
CB A:CYS111 3.3 10.3 1.0
CB A:CYS97 3.4 13.7 1.0
CB A:CYS103 3.4 11.2 1.0
CB A:CYS100 3.4 14.2 1.0
N A:CYS97 3.5 11.6 1.0
CA A:CYS111 3.7 10.0 1.0
N A:CYS100 3.9 13.9 1.0
CA A:CYS97 3.9 13.4 1.0
N A:GLY98 4.0 13.1 1.0
N A:LEU112 4.0 11.4 1.0
N A:CYS103 4.2 11.5 1.0
CA A:CYS100 4.2 13.5 1.0
C A:CYS111 4.3 10.8 1.0
C A:CYS97 4.3 13.1 1.0
CA A:CYS103 4.3 10.8 1.0
N A:LYS99 4.5 15.6 1.0
C A:GLN96 4.6 11.9 1.0
C A:CYS100 4.8 13.7 1.0
N A:LYS113 4.9 11.2 1.0
CG A:LYS113 4.9 15.2 1.0
O A:CYS100 4.9 13.7 1.0
O A:HOH552 4.9 29.4 1.0
CA A:GLN96 5.0 10.7 1.0
CA A:GLY98 5.0 14.2 1.0

Zinc binding site 3 out of 4 in 4nfs

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Zinc binding site 3 out of 4 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,2, 2-Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:15.1
occ:0.60
 O B:ETF378 2.0 16.4 0.8
NE2 B:HIS67 2.2 20.1 1.0
SG B:CYS174 2.3 17.3 1.0
SG B:CYS46 2.3 17.4 0.8
O B:HOH995 2.8 20.1 0.5
C2 B:ETF378 3.0 16.2 0.8
CE1 B:HIS67 3.2 16.2 1.0
CD2 B:HIS67 3.2 18.1 1.0
CB B:CYS174 3.4 13.2 1.0
CB B:CYS46 3.5 21.5 0.8
C5N B:NAJ377 3.6 12.8 1.0
OG B:SER48 3.7 15.1 1.0
SG B:CYS46 3.7 17.2 0.2
CB B:CYS46 3.8 14.8 0.2
C4N B:NAJ377 3.9 14.6 1.0
CB B:SER48 3.9 15.3 1.0
C6N B:NAJ377 4.2 12.5 1.0
ND1 B:HIS67 4.3 13.5 1.0
O B:HOH994 4.3 17.4 0.6
CG B:HIS67 4.3 13.6 1.0
C1 B:ETF378 4.4 20.2 0.8
F3 B:ETF378 4.6 25.8 0.8
CA B:CYS174 4.7 12.4 1.0
CE2 B:PHE93 4.8 14.0 1.0
F1 B:ETF378 4.8 24.8 0.8
N B:SER48 4.9 13.4 1.0
CZ B:PHE93 5.0 13.4 1.0
NH2 B:ARG369 5.0 15.7 0.6
C3N B:NAJ377 5.0 11.2 1.0

Zinc binding site 4 out of 4 in 4nfs

Go back to Zinc Binding Sites List in 4nfs
Zinc binding site 4 out of 4 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad and 2,2, 2-Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:13.9
occ:1.00
 SG B:CYS111 2.3 13.6 1.0
SG B:CYS97 2.3 16.4 1.0
SG B:CYS100 2.3 14.6 1.0
SG B:CYS103 2.4 13.2 1.0
CB B:CYS111 3.3 12.3 1.0
CB B:CYS100 3.4 16.3 1.0
CB B:CYS103 3.4 14.1 1.0
CB B:CYS97 3.4 16.3 1.0
N B:CYS97 3.5 14.1 1.0
CA B:CYS111 3.7 11.7 1.0
N B:CYS100 3.8 16.4 1.0
CA B:CYS97 3.9 15.5 1.0
N B:LEU112 4.0 12.8 1.0
N B:GLY98 4.0 15.7 1.0
N B:CYS103 4.2 13.0 1.0
CA B:CYS100 4.2 15.7 1.0
C B:CYS111 4.3 12.8 1.0
C B:CYS97 4.3 16.3 1.0
CA B:CYS103 4.4 12.8 1.0
N B:LYS99 4.5 17.1 1.0
C B:GLN96 4.6 12.3 1.0
N B:LYS113 4.8 14.0 1.0
C B:CYS100 4.9 15.6 1.0
CG B:LYS113 4.9 17.8 1.0
O B:CYS100 4.9 14.4 1.0
O B:HOH482 4.9 30.4 1.0
CA B:GLY98 4.9 16.9 1.0
CA B:GLN96 4.9 11.9 1.0
C B:LYS99 5.0 18.9 1.0

Reference:

A.Yahashiri, J.K.Rubach, B.V.Plapp. Effects of Cavities at the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase on Structure, Dynamics and Catalysis. Biochemistry V. 53 881 2014.
ISSN: ISSN 0006-2960
PubMed: 24437493
DOI: 10.1021/BI401583F
Page generated: Sun Oct 27 03:06:55 2024

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