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Zinc in PDB 4cpd: Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1

Enzymatic activity of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1

All present enzymatic activity of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1:
1.1.1.1;

Protein crystallography data

The structure of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1, PDB code: 4cpd was solved by H.Man, S.Gargulio, A.Frank, F.Hollmann, G.Grogan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 112.52 / 2.74
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 87.367, 87.367, 337.560, 90.00, 90.00, 120.00
R / Rfree (%) 19.157 / 24.758

Zinc Binding Sites:

The binding sites of Zinc atom in the Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1 (pdb code 4cpd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1, PDB code: 4cpd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4cpd

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Zinc binding site 1 out of 8 in the Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1200

b:44.0
occ:1.00
 OD2 A:ASP152 1.9 47.0 1.0
SG A:CYS38 2.2 40.9 1.0
NE2 A:HIS59 2.3 43.7 1.0
O A:HOH2015 2.5 32.0 1.0
CG A:ASP152 2.9 41.9 1.0
CD2 A:HIS59 3.0 38.9 1.0
CB A:CYS38 3.1 44.4 1.0
OD1 A:ASP152 3.2 47.9 1.0
CE1 A:HIS59 3.4 47.0 1.0
OG A:SER40 3.7 54.0 1.0
C5N A:NAD1407 3.9 67.3 1.0
CB A:SER40 4.1 47.9 1.0
CB A:ASP152 4.2 39.5 1.0
CG A:HIS59 4.2 40.6 1.0
ND1 A:HIS59 4.4 47.5 1.0
CG A:GLU60 4.5 39.8 1.0
CA A:CYS38 4.6 48.0 1.0
C6N A:NAD1407 4.6 74.1 1.0
CD A:GLU60 4.6 41.3 1.0
C4N A:NAD1407 4.7 63.7 1.0
CG2 A:ILE153 4.7 42.0 1.0
O A:HOH2011 4.9 37.2 1.0
CG A:PHE85 4.9 48.4 1.0
OE1 A:GLU60 4.9 41.6 1.0
N A:SER40 4.9 48.6 1.0
CD2 A:PHE85 5.0 50.5 1.0

Zinc binding site 2 out of 8 in 4cpd

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Zinc binding site 2 out of 8 in the Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1300

b:38.7
occ:1.00
 SG A:CYS103 2.2 41.6 1.0
SG A:CYS89 2.3 47.7 1.0
SG A:CYS95 2.3 39.0 1.0
SG A:CYS92 2.4 37.1 1.0
CB A:CYS103 3.2 41.1 1.0
CB A:CYS89 3.3 42.3 1.0
CB A:CYS92 3.4 34.4 1.0
N A:CYS89 3.4 38.1 1.0
CB A:CYS95 3.5 40.1 1.0
CA A:CYS103 3.6 42.5 1.0
N A:GLY90 3.7 34.6 1.0
N A:CYS92 3.8 38.7 1.0
CA A:CYS89 3.8 38.5 1.0
N A:GLU104 3.9 51.4 1.0
CA A:CYS92 4.2 36.1 1.0
C A:CYS103 4.2 45.7 1.0
C A:CYS89 4.2 36.5 1.0
N A:CYS95 4.3 37.5 1.0
N A:THR91 4.4 39.2 1.0
CA A:CYS95 4.4 37.3 1.0
C A:ALA88 4.5 38.9 1.0
N A:ARG105 4.6 53.2 1.0
CA A:GLY90 4.7 35.0 1.0
CA A:ALA88 4.8 36.6 1.0
O A:CYS92 4.8 41.5 1.0
C A:CYS92 4.8 42.1 1.0
N A:CYS103 4.9 40.5 1.0
C A:THR91 4.9 38.6 1.0
C A:GLY90 5.0 37.4 1.0
CB A:ALA88 5.0 37.1 1.0

Zinc binding site 3 out of 8 in 4cpd

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Zinc binding site 3 out of 8 in the Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1200

b:53.5
occ:1.00
 OD2 B:ASP152 2.0 50.2 1.0
NE2 B:HIS59 2.3 57.0 1.0
SG B:CYS38 2.4 50.1 1.0
CG B:ASP152 2.9 44.3 1.0
CD2 B:HIS59 3.0 54.0 1.0
OD1 B:ASP152 3.2 51.3 1.0
CB B:CYS38 3.4 51.5 1.0
CE1 B:HIS59 3.4 59.1 1.0
OG B:SER40 3.5 60.7 1.0
CG B:HIS59 4.2 52.6 1.0
CB B:ASP152 4.3 39.2 1.0
ND1 B:HIS59 4.4 58.7 1.0
CB B:SER40 4.7 57.4 1.0
CD B:GLU60 4.8 52.0 1.0
CD2 B:PHE85 4.8 44.4 1.0
CG B:GLU60 4.8 50.9 1.0
CG B:PHE85 4.8 45.2 1.0
CA B:CYS38 4.8 53.9 1.0
CG2 B:ILE153 4.9 47.1 1.0
OE1 B:GLU60 5.0 57.5 1.0

Zinc binding site 4 out of 8 in 4cpd

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Zinc binding site 4 out of 8 in the Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1300

b:40.8
occ:1.00
 SG B:CYS103 2.3 43.0 1.0
SG B:CYS89 2.3 40.2 1.0
SG B:CYS92 2.3 44.4 1.0
SG B:CYS95 2.3 41.2 1.0
CB B:CYS103 3.2 45.6 1.0
CB B:CYS92 3.3 38.3 1.0
CB B:CYS89 3.4 40.3 1.0
CB B:CYS95 3.4 39.8 1.0
N B:CYS89 3.5 39.7 1.0
CA B:CYS103 3.5 44.2 1.0
N B:GLY90 3.7 43.3 1.0
N B:CYS92 3.8 41.4 1.0
N B:GLU104 3.8 46.0 1.0
CA B:CYS89 3.9 41.5 1.0
CA B:CYS92 4.1 39.2 1.0
C B:CYS103 4.1 45.0 1.0
C B:CYS89 4.2 40.6 1.0
N B:CYS95 4.3 37.6 1.0
CA B:CYS95 4.4 36.7 1.0
N B:THR91 4.5 42.3 1.0
C B:ALA88 4.6 40.2 1.0
N B:ARG105 4.6 55.4 1.0
C B:CYS92 4.8 41.3 1.0
CA B:GLY90 4.8 40.2 1.0
CA B:ALA88 4.8 42.5 1.0
O B:CYS92 4.8 39.9 1.0
N B:CYS103 4.8 47.0 1.0
CB B:ALA88 5.0 40.9 1.0
C B:THR91 5.0 39.2 1.0
CA B:GLU104 5.0 49.1 1.0

Zinc binding site 5 out of 8 in 4cpd

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Zinc binding site 5 out of 8 in the Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1200

b:58.2
occ:1.00
 OD2 C:ASP152 1.7 47.9 1.0
O C:HOH2006 2.0 48.0 1.0
SG C:CYS38 2.2 61.0 1.0
NE2 C:HIS59 2.3 50.5 1.0
CG C:ASP152 2.8 50.4 1.0
CD2 C:HIS59 3.0 52.1 1.0
CB C:CYS38 3.1 62.8 1.0
OD1 C:ASP152 3.1 48.6 1.0
CE1 C:HIS59 3.4 50.8 1.0
OG C:SER40 3.8 58.9 1.0
C5N C:NAD1407 4.0 52.6 1.0
CB C:ASP152 4.1 50.1 1.0
CB C:SER40 4.2 59.1 1.0
CG C:HIS59 4.2 52.7 1.0
ND1 C:HIS59 4.4 55.9 1.0
CG C:GLU60 4.4 50.0 1.0
CD C:GLU60 4.5 56.2 1.0
CG2 C:ILE153 4.5 57.1 1.0
CA C:CYS38 4.6 64.3 1.0
C4N C:NAD1407 4.7 49.5 1.0
OE1 C:GLU60 4.7 63.6 1.0
C6N C:NAD1407 4.7 53.4 1.0
OE2 C:GLU60 4.9 59.0 1.0
N C:SER40 5.0 51.0 1.0
CG C:PHE85 5.0 53.6 1.0

Zinc binding site 6 out of 8 in 4cpd

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Zinc binding site 6 out of 8 in the Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1300

b:50.8
occ:1.00
 SG C:CYS95 2.2 47.1 1.0
SG C:CYS89 2.2 56.0 1.0
SG C:CYS92 2.3 45.6 1.0
SG C:CYS103 2.4 46.3 1.0
CB C:CYS103 3.3 49.8 1.0
CB C:CYS95 3.3 54.8 1.0
CB C:CYS92 3.3 44.5 1.0
CB C:CYS89 3.3 53.3 1.0
N C:CYS89 3.4 45.0 1.0
N C:GLY90 3.6 57.6 1.0
CA C:CYS103 3.7 50.2 1.0
N C:CYS92 3.7 47.7 1.0
CA C:CYS89 3.8 49.7 1.0
CA C:CYS92 4.1 47.6 1.0
N C:GLU104 4.1 59.0 1.0
C C:CYS89 4.1 50.6 1.0
N C:CYS95 4.2 48.3 1.0
N C:THR91 4.3 54.1 1.0
CA C:CYS95 4.3 54.2 1.0
C C:CYS103 4.3 54.2 1.0
C C:ALA88 4.5 47.7 1.0
CA C:GLY90 4.6 60.5 1.0
O C:CYS92 4.7 48.1 1.0
C C:CYS92 4.7 54.8 1.0
CA C:ALA88 4.8 50.4 1.0
N C:ARG105 4.8 56.9 1.0
C C:GLY90 4.8 60.3 1.0
C C:THR91 4.9 50.1 1.0
CB C:ALA88 4.9 54.4 1.0
N C:CYS103 5.0 48.0 1.0

Zinc binding site 7 out of 8 in 4cpd

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Zinc binding site 7 out of 8 in the Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1200

b:61.5
occ:1.00
 OD2 D:ASP152 2.0 46.8 1.0
NE2 D:HIS59 2.3 52.2 1.0
SG D:CYS38 2.4 69.8 1.0
CG D:ASP152 2.9 45.0 1.0
O D:HOH2004 2.9 53.7 1.0
CD2 D:HIS59 3.1 52.3 1.0
OD1 D:ASP152 3.1 43.8 1.0
CB D:CYS38 3.3 72.8 1.0
CE1 D:HIS59 3.4 54.4 1.0
OG D:SER40 3.6 84.8 1.0
C5N D:NAD1407 3.9 62.4 1.0
CB D:SER40 4.0 87.8 1.0
CG D:HIS59 4.3 51.3 1.0
CB D:ASP152 4.3 40.2 1.0
ND1 D:HIS59 4.4 51.3 1.0
C6N D:NAD1407 4.6 66.9 1.0
C4N D:NAD1407 4.6 61.9 1.0
CG2 D:ILE153 4.7 43.1 1.0
CA D:CYS38 4.8 68.5 1.0
CG D:GLU60 4.8 52.0 1.0
CD D:GLU60 4.8 52.1 1.0
CD2 D:PHE85 4.8 49.7 1.0
CG D:PHE85 4.9 50.5 1.0
N D:SER40 4.9 79.9 1.0
OE1 D:GLU60 4.9 50.2 1.0

Zinc binding site 8 out of 8 in 4cpd

Go back to Zinc Binding Sites List in 4cpd
Zinc binding site 8 out of 8 in the Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1300

b:50.6
occ:1.00
 SG D:CYS92 2.2 51.2 1.0
SG D:CYS95 2.2 42.3 1.0
SG D:CYS103 2.3 49.9 1.0
SG D:CYS89 2.4 62.1 1.0
CB D:CYS103 3.1 57.1 1.0
CB D:CYS92 3.3 47.4 1.0
CB D:CYS95 3.4 42.0 1.0
N D:CYS89 3.5 57.4 1.0
CA D:CYS103 3.5 54.3 1.0
CB D:CYS89 3.5 61.2 1.0
N D:GLY90 3.7 52.9 1.0
N D:CYS92 3.8 48.2 1.0
N D:GLU104 3.9 59.3 1.0
CA D:CYS89 3.9 58.4 1.0
CA D:CYS92 4.1 44.8 1.0
C D:CYS103 4.1 55.0 1.0
N D:CYS95 4.2 40.2 1.0
C D:CYS89 4.3 53.2 1.0
CA D:CYS95 4.3 40.2 1.0
N D:THR91 4.5 49.5 1.0
C D:ALA88 4.6 59.2 1.0
N D:ARG105 4.7 57.0 1.0
C D:CYS92 4.7 44.9 1.0
N D:CYS103 4.7 48.1 1.0
O D:CYS92 4.7 46.5 1.0
CA D:GLY90 4.8 50.6 1.0
CA D:ALA88 4.8 59.7 1.0
C D:THR91 5.0 47.4 1.0
C D:GLY90 5.0 49.2 1.0

Reference:

H.Man, S.Gargulio, A.Frank, F.Hollmann, G.Grogan. Structure of the Nadh-Dependent Thermostable Alcohol Dehydrogenase Tadh From Thermus Sp. ATN1 Provides A Platform For Engineering Specificity and Improved Compatibility with Inorganic Cofactor-Regeneration Catalysts J.Mol.Catal., B Enzym. V. 105 1 2014.
ISSN: ISSN 1381-1177
DOI: 10.1016/J.MOLCATB.2014.03.013
Page generated: Sat Oct 26 20:57:59 2024

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