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Zinc in PDB 7rm6: Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide

Enzymatic activity of Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide, PDB code: 7rm6 was solved by C.Zheng, S.G.Boxer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.94 / 1.43
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.142, 50.979, 92.864, 92.41, 103.03, 108.94
R / Rfree (%) 19 / 20.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide (pdb code 7rm6). 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 in Complex with Nadh and N- Cylcohexyl Formamide, PDB code: 7rm6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7rm6

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Zinc binding site 1 out of 4 in the Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide


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 in Complex with Nadh and N- Cylcohexyl Formamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:20.3
occ:1.00
NE2 A:HIS67 2.2 19.8 1.0
O9 A:CXF404 2.2 20.4 1.0
SG A:CYS46 2.2 19.9 1.0
SG A:CYS174 2.3 19.3 1.0
C7 A:CXF404 2.8 20.6 1.0
CD2 A:HIS67 3.1 20.4 1.0
CE1 A:HIS67 3.2 17.5 1.0
CB A:CYS46 3.3 19.1 1.0
CB A:CYS174 3.3 17.2 1.0
C5N A:NAI403 3.4 17.8 1.0
OG A:SER48 3.9 18.5 1.0
CB A:SER48 4.0 17.5 1.0
C6N A:NAI403 4.1 17.3 1.0
C4N A:NAI403 4.2 17.9 1.0
N8 A:CXF404 4.2 23.5 1.0
ND1 A:HIS67 4.3 21.3 1.0
CG A:HIS67 4.3 18.2 1.0
NH2 A:ARG369 4.6 21.6 1.0
CA A:CYS174 4.7 16.8 1.0
CA A:CYS46 4.7 17.9 1.0
N A:GLY175 4.9 21.1 1.0
N A:SER48 4.9 19.5 1.0
OE2 A:GLU68 4.9 20.5 1.0

Zinc binding site 2 out of 4 in 7rm6

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Zinc binding site 2 out of 4 in the Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide


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 in Complex with Nadh and N- Cylcohexyl Formamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:22.7
occ:1.00
SG A:CYS111 2.3 21.0 1.0
SG A:CYS100 2.3 23.2 1.0
SG A:CYS103 2.3 23.0 1.0
SG A:CYS97 2.3 24.9 1.0
CB A:CYS111 3.3 20.8 1.0
CB A:CYS97 3.4 22.8 1.0
CB A:CYS100 3.4 26.8 1.0
CB A:CYS103 3.4 27.0 1.0
N A:CYS97 3.6 21.4 1.0
CA A:CYS111 3.7 19.5 1.0
N A:CYS100 3.9 24.9 1.0
CA A:CYS97 3.9 24.9 1.0
N A:GLY98 4.0 24.9 1.0
N A:LEU112 4.0 21.7 1.0
CA A:CYS100 4.2 26.0 1.0
N A:CYS103 4.3 23.3 1.0
C A:CYS111 4.3 20.5 1.0
C A:CYS97 4.3 26.5 1.0
CA A:CYS103 4.4 25.9 1.0
N A:LYS99 4.6 29.1 1.0
C A:GLN96 4.7 23.9 1.0
CG A:LYS113 4.8 27.4 1.0
C A:CYS100 4.8 25.1 1.0
N A:LYS113 4.9 22.5 1.0
O A:CYS100 4.9 25.8 1.0
CA A:GLY98 5.0 27.9 1.0
CA A:GLN96 5.0 22.6 1.0
C A:LYS99 5.0 27.9 1.0

Zinc binding site 3 out of 4 in 7rm6

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Zinc binding site 3 out of 4 in the Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide


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 in Complex with Nadh and N- Cylcohexyl Formamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:23.1
occ:1.00
NE2 B:HIS67 2.2 23.2 1.0
O9 B:CXF404 2.2 23.9 1.0
SG B:CYS174 2.3 22.6 1.0
SG B:CYS46 2.3 23.9 1.0
C7 B:CXF404 2.9 22.8 1.0
CD2 B:HIS67 3.1 22.5 1.0
CE1 B:HIS67 3.2 24.6 1.0
CB B:CYS46 3.3 20.1 1.0
CB B:CYS174 3.3 20.5 1.0
C5N B:NAI403 3.6 21.5 1.0
CB B:SER48 3.9 25.1 1.0
OG B:SER48 4.0 22.4 1.0
C4N B:NAI403 4.1 21.7 1.0
C6N B:NAI403 4.1 21.5 1.0
N8 B:CXF404 4.2 24.6 1.0
ND1 B:HIS67 4.2 25.7 1.0
CG B:HIS67 4.3 22.4 1.0
NH2 B:ARG369 4.5 23.7 1.0
CA B:CYS174 4.7 22.4 1.0
CA B:CYS46 4.7 21.4 1.0
N B:GLY175 4.9 22.1 1.0
N B:SER48 4.9 23.1 1.0
CE2 B:PHE93 4.9 25.4 1.0
OE2 B:GLU68 5.0 22.6 1.0

Zinc binding site 4 out of 4 in 7rm6

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Zinc binding site 4 out of 4 in the Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide


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 in Complex with Nadh and N- Cylcohexyl Formamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:25.1
occ:1.00
SG B:CYS103 2.3 23.5 1.0
SG B:CYS111 2.3 24.4 1.0
SG B:CYS97 2.3 27.2 1.0
SG B:CYS100 2.4 27.4 1.0
CB B:CYS111 3.2 23.0 1.0
CB B:CYS103 3.4 23.5 1.0
CB B:CYS100 3.4 25.7 1.0
CB B:CYS97 3.5 24.2 1.0
N B:CYS97 3.6 24.6 1.0
CA B:CYS111 3.8 22.4 1.0
N B:CYS100 3.9 27.7 1.0
N B:GLY98 3.9 26.1 1.0
CA B:CYS97 3.9 28.5 1.0
N B:LEU112 4.0 23.5 1.0
CA B:CYS100 4.2 29.1 1.0
N B:CYS103 4.3 23.6 1.0
C B:CYS111 4.3 23.3 1.0
CA B:CYS103 4.4 25.2 1.0
C B:CYS97 4.4 23.5 1.0
N B:LYS99 4.5 28.0 1.0
C B:GLN96 4.6 25.0 1.0
C B:CYS100 4.8 27.1 1.0
CA B:GLY98 4.9 27.1 1.0
O B:CYS100 4.9 27.1 1.0
N B:LYS113 4.9 25.1 1.0
CA B:GLN96 4.9 22.6 1.0
CG B:LYS113 5.0 31.7 1.0

Reference:

C.Zheng, Y.Mao, J.Kozuch, A.O.Atsango, Z.Ji, T.E.Markland, S.G.Boxer. A Two-Directional Vibrational Probe Reveals Different Electric Field Orientations in Solution and An Enzyme Active Site. Nat.Chem. V. 14 891 2022.
ISSN: ESSN 1755-4349
PubMed: 35513508
DOI: 10.1038/S41557-022-00937-W
Page generated: Sat Apr 8 02:52:07 2023

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