Zinc in PDB 8g2l: Horse Liver Alcohol Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol

Enzymatic activity of Horse Liver Alcohol Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol

All present enzymatic activity of Horse Liver Alcohol Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol, PDB code: 8g2l 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) 19.88 / 1.42
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.02, 51.08, 92.61, 92.08, 103, 109.44
R / Rfree (%) 18.6 / 21.1

Other elements in 8g2l:

The structure of Horse Liver Alcohol Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol (pdb code 8g2l). 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 Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol, PDB code: 8g2l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8g2l

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Zinc binding site 1 out of 4 in the Horse Liver Alcohol Dehydrogense His-51 Gln Form 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 Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:18.5
occ:1.00
 O A:ETF404 1.9 16.4 0.4
NE2 A:HIS67 2.1 14.9 1.0
O A:ETF404 2.1 14.8 0.6
SG A:CYS174 2.3 17.4 1.0
SG A:CYS46 2.3 17.5 1.0
C2 A:ETF404 2.9 15.9 0.6
CD2 A:HIS67 3.0 16.0 1.0
C2 A:ETF404 3.0 17.5 0.4
CE1 A:HIS67 3.2 15.5 1.0
CB A:CYS46 3.3 16.6 1.0
C5N A:NAJ403 3.3 13.2 1.0
CB A:CYS174 3.4 16.7 1.0
C4N A:NAJ403 3.8 13.6 1.0
OG A:SER48 3.8 15.0 1.0
C6N A:NAJ403 3.9 14.2 1.0
F3 A:ETF404 4.0 19.6 0.4
CB A:SER48 4.0 14.9 1.0
C1 A:ETF404 4.1 19.2 0.4
CG A:HIS67 4.2 16.8 1.0
ND1 A:HIS67 4.2 16.4 1.0
C1 A:ETF404 4.3 17.8 0.6
F3 A:ETF404 4.5 19.2 0.6
NH2 A:ARG369 4.7 17.7 1.0
CA A:CYS46 4.7 16.8 1.0
CA A:CYS174 4.8 14.4 1.0
F1 A:ETF404 4.8 19.2 0.4
F1 A:ETF404 4.8 19.7 0.6
OE2 A:GLU68 4.9 17.8 1.0
N1N A:NAJ403 4.9 14.1 1.0
N A:SER48 4.9 15.4 1.0
CE2 A:PHE93 4.9 16.2 1.0
C3N A:NAJ403 5.0 13.4 1.0

Zinc binding site 2 out of 4 in 8g2l

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Zinc binding site 2 out of 4 in the Horse Liver Alcohol Dehydrogense His-51 Gln Form 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 Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:18.5
occ:1.00
 SG A:CYS100 2.3 19.0 1.0
SG A:CYS111 2.3 18.6 1.0
SG A:CYS103 2.4 18.1 1.0
SG A:CYS97 2.4 20.3 1.0
CB A:CYS111 3.3 20.1 1.0
CB A:CYS97 3.4 19.4 1.0
CB A:CYS103 3.4 19.2 1.0
CB A:CYS100 3.4 22.7 1.0
N A:CYS97 3.6 18.6 1.0
CA A:CYS111 3.7 17.7 1.0
N A:CYS100 3.9 21.5 1.0
CA A:CYS97 3.9 18.8 1.0
N A:GLY98 4.0 20.5 1.0
N A:LEU112 4.0 18.5 1.0
N A:CYS103 4.1 18.0 1.0
CA A:CYS100 4.2 19.2 1.0
C A:CYS111 4.3 18.7 1.0
CA A:CYS103 4.3 19.5 1.0
C A:CYS97 4.3 20.7 1.0
N A:LYS99 4.6 23.7 1.0
C A:GLN96 4.6 17.6 1.0
N A:LYS113 4.8 16.9 1.0
O A:HOH814 4.9 39.0 1.0
C A:CYS100 4.9 19.4 1.0
O A:CYS100 4.9 20.2 1.0
CG A:LYS113 4.9 23.9 1.0
CA A:GLN96 5.0 16.6 1.0

Zinc binding site 3 out of 4 in 8g2l

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Zinc binding site 3 out of 4 in the Horse Liver Alcohol Dehydrogense His-51 Gln Form 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 Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:21.3
occ:1.00
 O B:ETF404 2.0 17.5 0.6
O B:ETF404 2.0 15.5 0.4
NE2 B:HIS67 2.1 19.5 1.0
SG B:CYS174 2.3 20.1 1.0
SG B:CYS46 2.4 18.8 1.0
C2 B:ETF404 2.8 19.2 0.6
CD2 B:HIS67 3.0 17.4 1.0
CE1 B:HIS67 3.1 21.2 1.0
C2 B:ETF404 3.3 18.1 0.4
CB B:CYS46 3.3 19.3 1.0
C5N B:NAJ403 3.4 15.0 1.0
CB B:CYS174 3.4 17.5 1.0
OG B:SER48 3.8 17.8 1.0
C6N B:NAJ403 3.8 14.6 1.0
C4N B:NAJ403 3.8 15.7 1.0
CB B:SER48 3.9 18.0 1.0
F3 B:ETF404 4.1 24.8 0.4
ND1 B:HIS67 4.2 19.5 1.0
CG B:HIS67 4.2 18.1 1.0
C1 B:ETF404 4.2 21.6 0.6
C1 B:ETF404 4.2 19.8 0.4
F3 B:ETF404 4.6 21.2 0.6
NH2 B:ARG369 4.6 23.9 1.0
F1 B:ETF404 4.7 23.2 0.6
CA B:CYS46 4.8 19.5 1.0
CA B:CYS174 4.8 17.4 1.0
F1 B:ETF404 4.8 18.1 0.4
CE2 B:PHE93 4.8 17.8 1.0
N B:SER48 4.9 18.6 1.0
OE2 B:GLU68 4.9 20.4 1.0
N1N B:NAJ403 4.9 15.3 1.0
CA B:SER48 5.0 17.8 1.0

Zinc binding site 4 out of 4 in 8g2l

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Zinc binding site 4 out of 4 in the Horse Liver Alcohol Dehydrogense His-51 Gln Form 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 Dehydrogense His-51 Gln Form Complexed with Nad+ and 2,2,2-Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:20.2
occ:1.00
 SG B:CYS100 2.3 20.5 1.0
SG B:CYS111 2.3 20.8 1.0
SG B:CYS97 2.4 21.5 1.0
SG B:CYS103 2.4 19.7 1.0
CB B:CYS111 3.2 21.6 1.0
CB B:CYS103 3.4 18.6 1.0
CB B:CYS100 3.4 23.4 1.0
CB B:CYS97 3.5 18.9 1.0
N B:CYS97 3.6 19.8 1.0
CA B:CYS111 3.7 19.2 1.0
N B:CYS100 3.8 23.0 1.0
CA B:CYS97 3.9 21.1 1.0
N B:GLY98 4.0 23.7 1.0
N B:LEU112 4.0 20.7 1.0
CA B:CYS100 4.2 22.3 1.0
N B:CYS103 4.2 18.1 1.0
C B:CYS111 4.3 18.6 1.0
C B:CYS97 4.4 23.0 1.0
CA B:CYS103 4.4 19.3 1.0
N B:LYS99 4.4 24.1 1.0
C B:GLN96 4.6 18.4 1.0
N B:LYS113 4.9 21.7 1.0
CA B:GLN96 4.9 19.2 1.0
C B:CYS100 4.9 19.1 1.0
CG B:LYS113 4.9 23.9 1.0
O B:HOH766 4.9 32.8 1.0
O B:CYS100 5.0 21.4 1.0
C B:LYS99 5.0 30.3 1.0

Reference:

B.V.Plapp, E.G.Kovaleva. Histidine-51 Facilitates Deprotonation of the Zinc-Bound Ligand During Catalysis By Horse Liver Alcohol Dehydrogenase To Be Published.
Page generated: Sat Apr 8 08:59:21 2023

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