Zinc in PDB 7jnq: Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso
Enzymatic activity of Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso
All present enzymatic activity of Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso:
1.1.1.2;
Protein crystallography data
The structure of Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso, PDB code: 7jnq
was solved by
T.Dinh,
R.Phillips,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
68.84 /
1.87
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.590,
125.130,
137.150,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.3 /
22.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso
(pdb code 7jnq). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso, PDB code: 7jnq:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7jnq
Go back to
Zinc Binding Sites List in 7jnq
Zinc binding site 1 out
of 4 in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:45.8
occ:0.67
|
OD2
|
A:ASP150
|
1.9
|
73.2
|
1.0
|
NE2
|
A:HIS59
|
2.1
|
79.8
|
1.0
|
O
|
A:DMS404
|
2.3
|
67.6
|
0.8
|
SG
|
A:CYS37
|
2.3
|
59.2
|
1.0
|
H5N
|
A:NAP402
|
2.5
|
80.1
|
0.9
|
CG
|
A:ASP150
|
2.9
|
66.3
|
1.0
|
CE1
|
A:HIS59
|
2.9
|
79.1
|
1.0
|
C5N
|
A:NAP402
|
3.1
|
66.4
|
0.9
|
HE1
|
A:HIS59
|
3.1
|
95.4
|
1.0
|
CD2
|
A:HIS59
|
3.1
|
77.9
|
1.0
|
HB2
|
A:CYS37
|
3.2
|
71.8
|
1.0
|
CB
|
A:CYS37
|
3.2
|
59.5
|
1.0
|
OD1
|
A:ASP150
|
3.3
|
66.8
|
1.0
|
HD2
|
A:HIS59
|
3.3
|
93.8
|
1.0
|
HB3
|
A:CYS37
|
3.4
|
71.8
|
1.0
|
HB2
|
A:SER39
|
3.4
|
99.2
|
1.0
|
S
|
A:DMS404
|
3.6
|
65.9
|
0.8
|
HG
|
A:SER39
|
3.6
|
0.4
|
1.0
|
C4N
|
A:NAP402
|
3.8
|
66.7
|
0.9
|
H4N
|
A:NAP402
|
3.8
|
80.5
|
0.9
|
C6N
|
A:NAP402
|
3.8
|
66.6
|
0.9
|
H6N
|
A:NAP402
|
3.8
|
80.3
|
0.9
|
HE1
|
A:MET151
|
3.8
|
68.8
|
1.0
|
OG
|
A:SER39
|
3.9
|
83.3
|
1.0
|
HE3
|
A:MET151
|
4.0
|
68.8
|
1.0
|
H12
|
A:DMS404
|
4.0
|
79.4
|
0.8
|
ND1
|
A:HIS59
|
4.0
|
78.7
|
1.0
|
OE1
|
A:GLU60
|
4.1
|
60.0
|
1.0
|
CB
|
A:SER39
|
4.1
|
82.3
|
1.0
|
CG
|
A:HIS59
|
4.2
|
77.4
|
1.0
|
CE
|
A:MET151
|
4.2
|
57.0
|
1.0
|
CB
|
A:ASP150
|
4.2
|
59.9
|
1.0
|
HE2
|
A:MET151
|
4.3
|
68.8
|
1.0
|
H
|
A:SER39
|
4.3
|
93.2
|
1.0
|
C1
|
A:DMS404
|
4.3
|
65.8
|
0.8
|
HB2
|
A:ASP150
|
4.4
|
72.2
|
1.0
|
HG2
|
A:GLU60
|
4.4
|
66.1
|
1.0
|
HB3
|
A:ASP150
|
4.4
|
72.2
|
1.0
|
H13
|
A:DMS404
|
4.5
|
79.4
|
0.8
|
HG3
|
A:GLU60
|
4.6
|
66.1
|
1.0
|
HB3
|
A:SER39
|
4.6
|
99.2
|
1.0
|
CD
|
A:GLU60
|
4.7
|
58.0
|
1.0
|
CA
|
A:CYS37
|
4.7
|
58.0
|
1.0
|
HD1
|
A:HIS59
|
4.8
|
94.8
|
1.0
|
CG
|
A:GLU60
|
4.8
|
54.7
|
1.0
|
HA
|
A:CYS37
|
4.9
|
70.0
|
1.0
|
C3N
|
A:NAP402
|
4.9
|
65.1
|
0.9
|
N1N
|
A:NAP402
|
4.9
|
67.7
|
0.9
|
|
Zinc binding site 2 out
of 4 in 7jnq
Go back to
Zinc Binding Sites List in 7jnq
Zinc binding site 2 out
of 4 in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:41.4
occ:0.61
|
OD2
|
B:ASP150
|
2.0
|
61.7
|
1.0
|
NE2
|
B:HIS59
|
2.1
|
67.9
|
1.0
|
O
|
B:DMS404
|
2.3
|
61.9
|
0.9
|
SG
|
B:CYS37
|
2.3
|
47.0
|
1.0
|
H5N
|
B:NAP402
|
2.7
|
71.1
|
0.8
|
CG
|
B:ASP150
|
2.9
|
54.3
|
1.0
|
CE1
|
B:HIS59
|
2.9
|
66.7
|
1.0
|
CD2
|
B:HIS59
|
3.1
|
65.3
|
1.0
|
HE1
|
B:HIS59
|
3.1
|
80.4
|
1.0
|
HB2
|
B:SER39
|
3.1
|
77.2
|
1.0
|
HB2
|
B:CYS37
|
3.2
|
61.1
|
1.0
|
OD1
|
B:ASP150
|
3.2
|
55.7
|
1.0
|
CB
|
B:CYS37
|
3.2
|
50.5
|
1.0
|
HG
|
B:SER39
|
3.3
|
77.6
|
1.0
|
C5N
|
B:NAP402
|
3.3
|
58.9
|
0.8
|
HB3
|
B:CYS37
|
3.3
|
61.1
|
1.0
|
HD2
|
B:HIS59
|
3.3
|
78.7
|
1.0
|
S
|
B:DMS404
|
3.4
|
61.8
|
0.9
|
H11
|
B:DMS404
|
3.4
|
75.6
|
0.9
|
OG
|
B:SER39
|
3.7
|
64.3
|
1.0
|
C1
|
B:DMS404
|
3.7
|
62.6
|
0.9
|
CB
|
B:SER39
|
3.9
|
64.0
|
1.0
|
H13
|
B:DMS404
|
3.9
|
75.6
|
0.9
|
HE1
|
B:MET151
|
3.9
|
48.0
|
1.0
|
H6N
|
B:NAP402
|
3.9
|
68.6
|
0.8
|
C6N
|
B:NAP402
|
4.0
|
56.8
|
0.8
|
C4N
|
B:NAP402
|
4.0
|
61.6
|
0.8
|
ND1
|
B:HIS59
|
4.0
|
65.7
|
1.0
|
H4N
|
B:NAP402
|
4.0
|
74.3
|
0.8
|
H
|
B:SER39
|
4.1
|
78.1
|
1.0
|
CG
|
B:HIS59
|
4.1
|
63.6
|
1.0
|
HE3
|
B:MET151
|
4.1
|
48.0
|
1.0
|
OE2
|
B:GLU60
|
4.2
|
61.5
|
1.0
|
CB
|
B:ASP150
|
4.2
|
46.8
|
1.0
|
HB2
|
B:ASP150
|
4.3
|
56.5
|
1.0
|
CE
|
B:MET151
|
4.3
|
39.6
|
1.0
|
HE2
|
B:MET151
|
4.4
|
48.0
|
1.0
|
HB3
|
B:SER39
|
4.4
|
77.2
|
1.0
|
HB3
|
B:ASP150
|
4.5
|
56.5
|
1.0
|
HG2
|
B:GLU60
|
4.5
|
68.5
|
1.0
|
HG3
|
B:GLU60
|
4.6
|
68.5
|
1.0
|
H12
|
B:DMS404
|
4.7
|
75.6
|
0.9
|
CA
|
B:CYS37
|
4.7
|
54.4
|
1.0
|
HD1
|
B:HIS59
|
4.7
|
79.3
|
1.0
|
CD
|
B:GLU60
|
4.8
|
59.5
|
1.0
|
N
|
B:SER39
|
4.8
|
64.8
|
1.0
|
CG
|
B:GLU60
|
4.8
|
56.7
|
1.0
|
HA
|
B:CYS37
|
4.9
|
65.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7jnq
Go back to
Zinc Binding Sites List in 7jnq
Zinc binding site 3 out
of 4 in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn403
b:25.6
occ:0.70
|
OD2
|
C:ASP150
|
1.8
|
33.0
|
1.0
|
NE2
|
C:HIS59
|
2.0
|
32.3
|
1.0
|
O
|
C:DMS405
|
2.2
|
34.7
|
0.8
|
SG
|
C:CYS37
|
2.2
|
32.0
|
1.0
|
H5N
|
C:NAP404
|
2.7
|
46.9
|
0.8
|
CE1
|
C:HIS59
|
3.0
|
31.2
|
1.0
|
CG
|
C:ASP150
|
3.0
|
27.1
|
1.0
|
CD2
|
C:HIS59
|
3.0
|
31.1
|
1.0
|
HB2
|
C:CYS37
|
3.0
|
38.5
|
1.0
|
CB
|
C:CYS37
|
3.1
|
31.7
|
1.0
|
HE1
|
C:HIS59
|
3.2
|
37.9
|
1.0
|
HB3
|
C:CYS37
|
3.2
|
38.5
|
1.0
|
HD2
|
C:HIS59
|
3.2
|
37.7
|
1.0
|
HB2
|
C:SER39
|
3.2
|
40.2
|
1.0
|
HG
|
C:SER39
|
3.3
|
44.5
|
1.0
|
C5N
|
C:NAP404
|
3.3
|
38.7
|
0.8
|
S
|
C:DMS405
|
3.5
|
44.4
|
0.8
|
OD1
|
C:ASP150
|
3.6
|
31.8
|
1.0
|
OG
|
C:SER39
|
3.6
|
36.8
|
1.0
|
H23
|
C:DMS405
|
3.8
|
56.2
|
0.8
|
HE1
|
C:MET151
|
3.9
|
32.2
|
1.0
|
CB
|
C:SER39
|
3.9
|
33.2
|
1.0
|
H6N
|
C:NAP404
|
3.9
|
42.3
|
0.8
|
C6N
|
C:NAP404
|
4.0
|
34.9
|
0.8
|
HE3
|
C:MET151
|
4.0
|
32.2
|
1.0
|
C4N
|
C:NAP404
|
4.1
|
38.2
|
0.8
|
H4N
|
C:NAP404
|
4.1
|
46.3
|
0.8
|
ND1
|
C:HIS59
|
4.1
|
32.5
|
1.0
|
H
|
C:SER39
|
4.1
|
34.0
|
1.0
|
C2
|
C:DMS405
|
4.1
|
46.5
|
0.8
|
CG
|
C:HIS59
|
4.1
|
30.1
|
1.0
|
CB
|
C:ASP150
|
4.2
|
19.6
|
1.0
|
CE
|
C:MET151
|
4.3
|
26.5
|
1.0
|
OE1
|
C:GLU60
|
4.3
|
26.2
|
1.0
|
HE2
|
C:MET151
|
4.3
|
32.2
|
1.0
|
HB3
|
C:ASP150
|
4.3
|
23.9
|
1.0
|
HB2
|
C:ASP150
|
4.3
|
23.9
|
1.0
|
H22
|
C:DMS405
|
4.4
|
56.2
|
0.8
|
HB3
|
C:SER39
|
4.4
|
40.2
|
1.0
|
HG3
|
C:GLU60
|
4.4
|
27.6
|
1.0
|
CA
|
C:CYS37
|
4.5
|
28.7
|
1.0
|
HG2
|
C:GLU60
|
4.6
|
27.6
|
1.0
|
CD
|
C:GLU60
|
4.6
|
23.1
|
1.0
|
HA
|
C:CYS37
|
4.8
|
34.9
|
1.0
|
CG
|
C:GLU60
|
4.8
|
22.6
|
1.0
|
N
|
C:SER39
|
4.8
|
28.0
|
1.0
|
HZ1
|
C:LYS346
|
4.8
|
37.0
|
1.0
|
HD1
|
C:HIS59
|
4.9
|
39.4
|
1.0
|
H21
|
C:DMS405
|
5.0
|
56.2
|
0.8
|
|
Zinc binding site 4 out
of 4 in 7jnq
Go back to
Zinc Binding Sites List in 7jnq
Zinc binding site 4 out
of 4 in the Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn802
b:27.1
occ:0.72
|
OD2
|
D:ASP150
|
1.8
|
35.7
|
1.0
|
NE2
|
D:HIS59
|
2.0
|
31.4
|
1.0
|
O
|
D:DMS806
|
2.1
|
35.4
|
0.9
|
SG
|
D:CYS37
|
2.2
|
31.8
|
1.0
|
H5N
|
D:NAP803
|
2.7
|
48.2
|
0.8
|
CG
|
D:ASP150
|
2.9
|
34.3
|
1.0
|
CE1
|
D:HIS59
|
3.0
|
31.7
|
1.0
|
CD2
|
D:HIS59
|
3.0
|
30.2
|
1.0
|
HB2
|
D:CYS37
|
3.0
|
41.2
|
1.0
|
CB
|
D:CYS37
|
3.1
|
34.0
|
1.0
|
HE1
|
D:HIS59
|
3.2
|
38.5
|
1.0
|
HD2
|
D:HIS59
|
3.2
|
36.7
|
1.0
|
HB3
|
D:CYS37
|
3.2
|
41.2
|
1.0
|
HB2
|
D:SER39
|
3.2
|
43.0
|
1.0
|
C5N
|
D:NAP803
|
3.3
|
39.9
|
0.8
|
HG
|
D:SER39
|
3.3
|
45.2
|
1.0
|
OD1
|
D:ASP150
|
3.4
|
35.9
|
1.0
|
S
|
D:DMS806
|
3.5
|
45.7
|
0.9
|
OG
|
D:SER39
|
3.7
|
37.3
|
1.0
|
HE1
|
D:MET151
|
3.8
|
31.2
|
1.0
|
CB
|
D:SER39
|
3.9
|
35.5
|
1.0
|
H6N
|
D:NAP803
|
3.9
|
46.3
|
0.8
|
C6N
|
D:NAP803
|
4.0
|
38.3
|
0.8
|
H12
|
D:DMS806
|
4.0
|
54.6
|
0.9
|
C4N
|
D:NAP803
|
4.0
|
40.6
|
0.8
|
H4N
|
D:NAP803
|
4.0
|
49.1
|
0.8
|
H
|
D:SER39
|
4.0
|
39.4
|
1.0
|
HE3
|
D:MET151
|
4.1
|
31.2
|
1.0
|
ND1
|
D:HIS59
|
4.1
|
31.0
|
1.0
|
CG
|
D:HIS59
|
4.1
|
28.3
|
1.0
|
CB
|
D:ASP150
|
4.2
|
29.9
|
1.0
|
C1
|
D:DMS806
|
4.2
|
45.1
|
0.9
|
OE2
|
D:GLU60
|
4.2
|
29.4
|
1.0
|
H13
|
D:DMS806
|
4.3
|
54.6
|
0.9
|
HB2
|
D:ASP150
|
4.3
|
36.3
|
1.0
|
CE
|
D:MET151
|
4.3
|
25.7
|
1.0
|
HB3
|
D:ASP150
|
4.3
|
36.3
|
1.0
|
HE2
|
D:MET151
|
4.3
|
31.2
|
1.0
|
HB3
|
D:SER39
|
4.5
|
43.0
|
1.0
|
HG2
|
D:GLU60
|
4.5
|
37.4
|
1.0
|
CA
|
D:CYS37
|
4.5
|
32.9
|
1.0
|
HG3
|
D:GLU60
|
4.5
|
37.4
|
1.0
|
CD
|
D:GLU60
|
4.6
|
28.1
|
1.0
|
HA
|
D:CYS37
|
4.7
|
39.9
|
1.0
|
CG
|
D:GLU60
|
4.8
|
30.8
|
1.0
|
N
|
D:SER39
|
4.8
|
32.5
|
1.0
|
HD1
|
D:HIS59
|
4.9
|
37.6
|
1.0
|
C2
|
D:DMS806
|
5.0
|
44.6
|
0.9
|
CA
|
D:SER39
|
5.0
|
32.6
|
1.0
|
H22
|
D:DMS806
|
5.0
|
54.0
|
0.9
|
|
Reference:
T.Dinh,
R.Phillips.
Crystal Structure of Secondary Alcohol Dehydrogenases From the Thermoanaerobacter Ethanolicus with Nadp and Transition-State Analogue Inhibitor Dmso To Be Published.
Page generated: Wed Dec 16 13:46:17 2020
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