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
Go back to
Zinc Binding Sites List in 7quy
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
Go back to
Zinc Binding Sites List in 7quy
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 Sites List in 7quy
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 Sites List in 7quy
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
Go back to
Zinc Binding Sites List in 7quy
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
Go back to
Zinc Binding Sites List in 7quy
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
|