Zinc in PDB 7u9n: S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide

Enzymatic activity of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide

All present enzymatic activity of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide:
1.1.1.1;

Protein crystallography data

The structure of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide, PDB code: 7u9n 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) 35.93 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.91, 68.656, 94.402, 89.65, 76, 88.99
R / Rfree (%) 21.3 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide (pdb code 7u9n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide, PDB code: 7u9n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7u9n

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Zinc binding site 1 out of 8 in the S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:41.0
occ:1.00
O9 A:CXF404 2.0 36.2 1.0
NE2 A:HIS67 2.3 36.1 1.0
SG A:CYS174 2.3 42.2 1.0
SG A:CYS46 2.3 40.0 1.0
C7 A:CXF404 2.7 40.1 1.0
CB A:CYS46 3.2 35.6 1.0
CD2 A:HIS67 3.2 37.2 1.0
C5N A:NAI403 3.2 37.3 1.0
CE1 A:HIS67 3.3 40.3 1.0
CB A:CYS174 3.4 40.0 1.0
C6N A:NAI403 4.0 36.3 1.0
N8 A:CXF404 4.0 38.3 1.0
C4N A:NAI403 4.0 33.5 1.0
CB A:ALA48 4.1 38.8 1.0
NH2 A:ARG369 4.4 41.4 1.0
CG A:HIS67 4.4 39.7 1.0
ND1 A:HIS67 4.4 38.2 1.0
CA A:CYS46 4.7 39.3 1.0
CA A:CYS174 4.7 41.0 1.0
OE2 A:GLU68 4.8 42.5 1.0
CE2 A:PHE93 4.9 34.4 1.0
C1 A:CXF404 4.9 40.2 1.0
N A:GLY175 4.9 38.2 1.0
N A:ALA48 4.9 44.4 1.0

Zinc binding site 2 out of 8 in 7u9n

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Zinc binding site 2 out of 8 in the S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:36.2
occ:1.00
SG A:CYS103 2.3 33.3 1.0
SG A:CYS100 2.3 33.0 1.0
SG A:CYS97 2.3 36.0 1.0
SG A:CYS111 2.4 28.0 1.0
CB A:CYS111 3.3 31.4 1.0
CB A:CYS97 3.4 30.2 1.0
CB A:CYS100 3.4 35.5 1.0
N A:CYS97 3.4 34.8 1.0
CB A:CYS103 3.4 34.9 1.0
N A:CYS100 3.8 35.0 1.0
CA A:CYS111 3.8 29.9 1.0
CA A:CYS97 3.8 39.4 1.0
N A:GLY98 3.8 38.6 1.0
N A:LEU112 4.0 30.5 1.0
CA A:CYS100 4.1 30.2 1.0
C A:CYS97 4.2 38.9 1.0
N A:CYS103 4.2 32.2 1.0
C A:CYS111 4.3 35.0 1.0
CA A:CYS103 4.4 32.8 1.0
N A:LYS99 4.5 40.5 1.0
C A:GLN96 4.5 34.5 1.0
CG A:LYS113 4.7 37.3 1.0
C A:CYS100 4.8 35.4 1.0
CA A:GLN96 4.8 35.2 1.0
N A:LYS113 4.8 36.9 1.0
CA A:GLY98 4.8 36.9 1.0
C A:LYS99 4.9 40.7 1.0

Zinc binding site 3 out of 8 in 7u9n

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Zinc binding site 3 out of 8 in the S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:44.1
occ:1.00
O9 B:CXF404 2.2 40.2 1.0
SG B:CYS174 2.3 41.2 1.0
NE2 B:HIS67 2.3 39.2 1.0
SG B:CYS46 2.4 42.0 1.0
C7 B:CXF404 2.7 44.9 1.0
CD2 B:HIS67 3.1 41.6 1.0
CB B:CYS46 3.1 34.9 1.0
CE1 B:HIS67 3.3 40.4 1.0
CB B:CYS174 3.4 42.4 1.0
C5N B:NAI403 3.4 33.8 1.0
N8 B:CXF404 4.1 48.7 1.0
C6N B:NAI403 4.1 40.2 1.0
CB B:ALA48 4.2 39.2 1.0
C4N B:NAI403 4.2 35.4 1.0
NH2 B:ARG369 4.3 38.0 1.0
CG B:HIS67 4.3 41.5 1.0
ND1 B:HIS67 4.4 40.6 1.0
CA B:CYS46 4.6 41.8 1.0
OE2 B:GLU68 4.7 43.2 1.0
CA B:CYS174 4.8 40.5 1.0
N B:GLY175 4.8 39.6 1.0
CE2 B:PHE93 4.9 34.6 1.0
C1 B:CXF404 5.0 45.3 1.0

Zinc binding site 4 out of 8 in 7u9n

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Zinc binding site 4 out of 8 in the S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:43.4
occ:1.00
SG B:CYS103 2.3 43.4 1.0
SG B:CYS100 2.3 42.5 1.0
SG B:CYS111 2.4 38.2 1.0
SG B:CYS97 2.4 45.5 1.0
CB B:CYS111 3.4 38.6 1.0
CB B:CYS100 3.4 45.8 1.0
CB B:CYS97 3.4 41.9 1.0
CB B:CYS103 3.5 42.5 1.0
N B:CYS97 3.5 46.6 1.0
N B:CYS100 3.7 48.8 1.0
CA B:CYS111 3.8 38.0 1.0
CA B:CYS97 3.9 46.7 1.0
N B:LEU112 4.0 40.7 1.0
N B:GLY98 4.0 49.1 1.0
CA B:CYS100 4.1 45.4 1.0
N B:CYS103 4.2 39.6 1.0
C B:CYS97 4.3 47.0 1.0
C B:CYS111 4.3 39.7 1.0
CA B:CYS103 4.4 44.5 1.0
N B:LYS99 4.5 50.4 1.0
C B:GLN96 4.6 42.8 1.0
CG B:LYS113 4.8 46.3 1.0
C B:CYS100 4.8 41.9 1.0
N B:LYS113 4.8 44.5 1.0
O B:CYS100 4.9 41.5 1.0
C B:LYS99 4.9 51.9 1.0
CA B:GLN96 4.9 42.1 1.0

Zinc binding site 5 out of 8 in 7u9n

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Zinc binding site 5 out of 8 in the S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:52.2
occ:1.00
O9 C:CXF404 2.1 50.0 1.0
NE2 C:HIS67 2.3 57.3 1.0
SG C:CYS174 2.3 48.3 1.0
SG C:CYS46 2.3 55.2 1.0
C7 C:CXF404 2.9 49.9 1.0
CD2 C:HIS67 3.1 50.5 1.0
CE1 C:HIS67 3.3 50.6 1.0
C5N C:NAI403 3.3 36.4 1.0
CB C:CYS46 3.3 56.5 1.0
CB C:CYS174 3.5 42.5 1.0
CB C:ALA48 4.0 52.2 1.0
C4N C:NAI403 4.1 43.9 1.0
C6N C:NAI403 4.1 40.5 1.0
NH2 C:ARG369 4.2 51.4 1.0
N8 C:CXF404 4.2 49.9 1.0
CG C:HIS67 4.3 59.1 1.0
ND1 C:HIS67 4.4 57.3 1.0
OE2 C:GLU68 4.7 45.6 1.0
CA C:CYS46 4.8 57.3 1.0
CA C:CYS174 4.8 39.6 1.0
N C:ALA48 4.9 57.7 1.0
N C:GLY175 5.0 39.4 1.0
C1 C:CXF404 5.0 51.7 1.0

Zinc binding site 6 out of 8 in 7u9n

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Zinc binding site 6 out of 8 in the S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:46.5
occ:1.00
O C:HOH503 2.0 53.8 1.0
SG C:CYS103 2.3 44.8 1.0
SG C:CYS100 2.3 48.2 1.0
SG C:CYS111 2.4 45.1 1.0
SG C:CYS97 2.4 45.4 1.0
CB C:CYS97 3.3 46.1 1.0
CB C:CYS100 3.4 52.3 1.0
CB C:CYS111 3.4 44.7 1.0
N C:CYS97 3.4 45.6 1.0
CB C:CYS103 3.5 49.3 1.0
N C:CYS100 3.8 51.4 1.0
CA C:CYS111 3.8 43.5 1.0
N C:GLY98 3.8 46.0 1.0
CA C:CYS97 3.8 47.3 1.0
N C:LEU112 4.0 45.0 1.0
CA C:CYS100 4.1 51.9 1.0
C C:CYS97 4.2 51.8 1.0
N C:CYS103 4.3 47.8 1.0
C C:CYS111 4.3 48.4 1.0
N C:LYS99 4.4 51.6 1.0
CA C:CYS103 4.5 43.3 1.0
C C:GLN96 4.5 50.7 1.0
CG C:LYS113 4.7 56.1 1.0
N C:LYS113 4.7 47.4 1.0
C C:CYS100 4.8 49.8 1.0
CA C:GLY98 4.8 50.0 1.0
CA C:GLN96 4.8 43.8 1.0
O C:CYS100 4.8 51.4 1.0
C C:LYS99 4.9 56.5 1.0
C C:GLY98 4.9 50.8 1.0

Zinc binding site 7 out of 8 in 7u9n

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Zinc binding site 7 out of 8 in the S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:65.0
occ:1.00
SG D:CYS174 2.2 46.8 1.0
O9 D:CXF404 2.3 62.3 1.0
NE2 D:HIS67 2.3 62.5 1.0
SG D:CYS46 2.3 70.2 1.0
C7 D:CXF404 3.0 59.2 1.0
CD2 D:HIS67 3.0 55.2 1.0
CB D:CYS46 3.1 77.3 1.0
CE1 D:HIS67 3.4 62.6 1.0
CB D:CYS174 3.4 52.0 1.0
C5N D:NAI403 3.6 55.5 1.0
CB D:ALA48 4.1 67.0 1.0
N8 D:CXF404 4.3 58.3 1.0
CG D:HIS67 4.3 53.4 1.0
C4N D:NAI403 4.3 52.6 1.0
NH2 D:ARG369 4.4 96.2 1.0
ND1 D:HIS67 4.4 56.1 1.0
CA D:CYS46 4.5 79.5 1.0
N D:ALA48 4.5 77.4 1.0
C6N D:NAI403 4.6 52.7 1.0
O D:HOH510 4.8 63.5 1.0
CA D:CYS174 4.8 55.2 1.0
C D:CYS46 4.9 79.8 1.0
OE2 D:GLU68 4.9 73.6 1.0
CA D:ALA48 5.0 71.5 1.0
N D:ARG47 5.0 84.7 1.0

Zinc binding site 8 out of 8 in 7u9n

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Zinc binding site 8 out of 8 in the S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of S48A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:43.6
occ:1.00
SG D:CYS103 2.3 42.8 1.0
SG D:CYS111 2.3 43.5 1.0
SG D:CYS100 2.3 39.9 1.0
SG D:CYS97 2.4 44.1 1.0
CB D:CYS97 3.3 45.8 1.0
CB D:CYS100 3.4 44.4 1.0
CB D:CYS103 3.4 45.9 1.0
N D:CYS97 3.4 45.2 1.0
CB D:CYS111 3.5 39.1 1.0
N D:CYS100 3.8 50.6 1.0
CA D:CYS97 3.8 47.5 1.0
CA D:CYS111 3.9 36.1 1.0
N D:GLY98 3.9 51.3 1.0
N D:LEU112 3.9 36.7 1.0
CA D:CYS100 4.1 43.6 1.0
N D:CYS103 4.2 36.6 1.0
C D:CYS97 4.3 53.3 1.0
C D:CYS111 4.3 43.3 1.0
CA D:CYS103 4.4 46.0 1.0
N D:LYS99 4.5 53.1 1.0
C D:GLN96 4.5 48.3 1.0
C D:CYS100 4.8 44.6 1.0
O D:CYS100 4.8 45.4 1.0
CA D:GLN96 4.8 45.9 1.0
N D:LYS113 4.8 38.6 1.0
CA D:GLY98 4.9 53.4 1.0
C D:LYS99 4.9 54.0 1.0
CG D:LYS113 5.0 48.7 1.0

Reference:

C.Zheng, S.G.Boxer. Structure of S48A Horse Liver Alcohol Dehydrogenase at 2.20 Angstroms Resolution To Be Published.
Page generated: Sat Apr 8 03:57:39 2023

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