Zinc in PDB 7quy: Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh

Enzymatic activity of Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh

All present enzymatic activity of Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh:
1.1.1.368;

Protein crystallography data

The structure of Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh, PDB code: 7quy was solved by M.L.Petchey, F.Stark, M.Ansorge-Schumacher, G.Grogan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.37 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 75.423, 239.331, 168.456, 90, 90, 90
R / Rfree (%) 21.5 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh (pdb code 7quy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh, PDB code: 7quy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7quy

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Zinc binding site 1 out of 6 in the Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:56.4
occ:1.00
 NE2 A:HIS65 2.0 60.8 1.0
OE2 A:GLU66 2.0 47.3 1.0
OD2 A:ASP156 2.0 60.7 1.0
SG A:CYS42 2.8 57.2 1.0
CD2 A:HIS65 2.9 61.0 1.0
CB A:CYS42 2.9 52.9 1.0
CE1 A:HIS65 3.0 59.3 1.0
CG A:ASP156 3.0 56.1 1.0
CD A:GLU66 3.0 49.6 1.0
CB A:ASP156 3.3 49.9 1.0
CG A:GLU66 3.4 48.0 1.0
NH2 A:ARG350 4.0 53.5 1.0
CG A:HIS65 4.0 55.5 1.0
ND1 A:HIS65 4.1 56.1 1.0
OD1 A:ASP156 4.2 63.8 1.0
OE1 A:GLU66 4.2 52.7 1.0
CA A:CYS42 4.4 57.1 1.0
OG1 A:THR44 4.5 64.2 1.0
CA A:ASP156 4.8 50.5 1.0
CB A:THR44 4.8 59.4 1.0
CB A:GLU66 4.9 43.0 1.0

Zinc binding site 2 out of 6 in 7quy

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Zinc binding site 2 out of 6 in the Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:70.2
occ:1.00
 SG A:CYS108 1.9 56.2 1.0
CB A:CYS94 2.3 54.9 1.0
SG A:CYS94 2.4 76.7 1.0
SG A:CYS100 2.4 52.6 1.0
SG A:CYS97 2.8 103.3 1.0
CB A:CYS97 3.2 58.1 1.0
CB A:CYS108 3.3 61.8 1.0
N A:CYS94 3.4 50.5 1.0
CA A:CYS94 3.5 52.2 1.0
O A:HOH512 3.8 49.0 1.0
CB A:CYS100 3.9 47.2 1.0
N A:CYS97 4.0 59.3 1.0
N A:GLY95 4.2 52.1 1.0
CA A:CYS97 4.2 64.7 1.0
C A:CYS94 4.3 57.4 1.0
CA A:CYS108 4.4 59.9 1.0
OD2 A:ASP110 4.4 83.6 1.0
CB A:ASP110 4.6 61.0 1.0
C A:PRO93 4.6 49.6 1.0
N A:THR96 4.7 50.4 1.0
N A:ASP110 4.7 61.5 1.0
N A:CYS100 4.8 51.7 1.0
N A:ARG109 4.8 65.5 1.0
CA A:CYS100 5.0 55.6 1.0
C A:CYS108 5.0 66.3 1.0

Zinc binding site 3 out of 6 in 7quy

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Zinc binding site 3 out of 6 in the Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:57.5
occ:1.00
 OD2 B:ASP156 2.0 68.3 1.0
OE2 B:GLU66 2.0 45.5 1.0
NE2 B:HIS65 2.1 60.6 1.0
SG B:CYS42 2.3 58.3 1.0
CB B:CYS42 3.0 62.8 1.0
CD2 B:HIS65 3.0 60.2 1.0
CG B:ASP156 3.0 56.3 1.0
CE1 B:HIS65 3.1 57.3 1.0
CD B:GLU66 3.1 51.1 1.0
CB B:ASP156 3.3 51.7 1.0
CG B:GLU66 3.5 48.0 1.0
NH2 B:ARG350 3.9 52.5 1.0
CG B:HIS65 4.1 57.9 1.0
ND1 B:HIS65 4.1 58.0 1.0
OD1 B:ASP156 4.2 57.8 1.0
OG1 B:THR44 4.2 70.5 1.0
OE1 B:GLU66 4.2 57.6 1.0
CA B:CYS42 4.3 63.9 1.0
CB B:THR44 4.8 64.0 1.0
CA B:ASP156 4.8 54.3 1.0

Zinc binding site 4 out of 6 in 7quy

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Zinc binding site 4 out of 6 in the Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn405

b:73.5
occ:1.00
 SG B:CYS108 1.8 61.0 1.0
SG B:CYS100 1.9 58.8 1.0
SG B:CYS94 2.3 53.8 1.0
SG B:CYS97 2.4 51.5 1.0
CB B:CYS94 2.6 46.7 1.0
CB B:CYS100 3.2 54.7 1.0
CB B:CYS108 3.2 51.0 1.0
N B:CYS94 3.4 51.4 1.0
CB B:CYS97 3.5 45.1 1.0
CA B:CYS94 3.6 49.2 1.0
O B:HOH511 3.8 31.5 1.0
N B:GLY95 3.8 51.0 1.0
N B:CYS97 4.0 46.8 1.0
N B:CYS100 4.1 52.5 1.0
CA B:CYS108 4.1 50.1 1.0
CA B:CYS100 4.1 52.0 1.0
C B:CYS94 4.2 51.6 1.0
CA B:CYS97 4.3 45.9 1.0
OD2 B:ASP110 4.3 87.5 1.0
C B:PRO93 4.4 44.7 1.0
N B:THR96 4.5 46.2 1.0
O B:CYS97 4.6 51.9 1.0
CB B:PRO93 4.6 47.8 1.0
C B:CYS97 4.7 51.7 1.0
CA B:PRO93 4.8 47.1 1.0
CA B:GLY95 4.8 50.3 1.0

Zinc binding site 5 out of 6 in 7quy

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Zinc binding site 5 out of 6 in the Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:65.3
occ:1.00
 OD2 C:ASP156 2.0 67.0 1.0
NE2 C:HIS65 2.1 59.5 1.0
OE2 C:GLU66 2.1 62.5 1.0
SG C:CYS42 2.3 50.0 1.0
CG C:ASP156 3.0 64.6 1.0
CB C:CYS42 3.0 69.5 1.0
CD2 C:HIS65 3.0 63.5 1.0
CD C:GLU66 3.1 64.3 1.0
CE1 C:HIS65 3.1 59.0 1.0
CB C:ASP156 3.3 63.0 1.0
CG C:GLU66 3.5 59.6 1.0
NH2 C:ARG350 4.0 58.9 1.0
OD1 C:ASP156 4.1 74.0 1.0
CG C:HIS65 4.1 64.9 1.0
ND1 C:HIS65 4.2 58.9 1.0
OE1 C:GLU66 4.2 71.1 1.0
CA C:CYS42 4.3 72.4 1.0
OG1 C:THR44 4.4 82.2 1.0
CB C:THR44 4.7 83.5 1.0
CA C:ASP156 4.7 61.5 1.0
CB C:GLU66 5.0 54.4 1.0
N C:ALA157 5.0 63.1 1.0

Zinc binding site 6 out of 6 in 7quy

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Zinc binding site 6 out of 6 in the Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Alcohol Dehydrogenase From Thauera Aromatica Complexed with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:120.5
occ:1.00
 SG C:CYS108 2.3 84.3 1.0
SG C:CYS97 2.3 157.1 1.0
SG C:CYS100 2.3 84.3 1.0
SG C:CYS94 2.5 99.1 1.0
CB C:CYS108 3.1 85.5 1.0
CB C:CYS97 3.3 131.7 1.0
CB C:CYS100 3.4 102.1 1.0
CB C:CYS94 3.5 87.3 1.0
CA C:CYS108 3.7 95.8 1.0
N C:CYS100 3.8 95.3 1.0
N C:CYS97 4.0 137.9 1.0
CA C:CYS97 4.1 133.3 1.0
N C:CYS94 4.1 103.2 1.0
CA C:CYS100 4.2 101.6 1.0
OD2 C:ASP110 4.3 122.0 1.0
CA C:CYS94 4.3 97.4 1.0
CB C:LEU99 4.4 93.3 1.0
N C:ARG109 4.6 92.3 1.0
N C:GLY95 4.6 104.0 1.0
C C:CYS97 4.6 130.8 1.0
C C:CYS108 4.7 91.5 1.0
O C:CYS97 4.8 108.7 1.0
C C:LEU99 4.8 99.7 1.0
C C:CYS94 4.9 102.6 1.0
N C:CYS108 4.9 101.9 1.0
N C:LEU99 4.9 100.3 1.0
CA C:LEU99 5.0 102.8 1.0

Reference:

F.Stark, C.Loderer, M.Petchey, G.Grogan, M.B.Ansorge-Schumacher. Advanced Insights Into Catalytic and Structural Features of the Zinc-Dependent Alcohol Dehydrogenase From Thauera Aromatica. Chembiochem V. 23 00149 2022.
ISSN: ESSN 1439-7633
PubMed: 35557486
DOI: 10.1002/CBIC.202200149
Page generated: Wed Oct 30 10:03:24 2024

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