Zinc in PDB 1yqx: Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution
Enzymatic activity of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution
All present enzymatic activity of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution:
1.1.1.195;
Protein crystallography data
The structure of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution, PDB code: 1yqx
was solved by
E.K.Bomati,
J.P.Noel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.33 /
2.50
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.362,
138.165,
67.629,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.2 /
27.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution
(pdb code 1yqx). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution, PDB code: 1yqx:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 1yqx
Go back to
Zinc Binding Sites List in 1yqx
Zinc binding site 1 out
of 4 in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1000
b:26.8
occ:1.00
|
SG
|
A:CYS50
|
2.4
|
23.9
|
1.0
|
SG
|
A:CYS166
|
2.4
|
27.2
|
1.0
|
NE2
|
A:HIS72
|
2.4
|
30.9
|
1.0
|
O
|
A:HOH2001
|
2.7
|
7.7
|
1.0
|
CE1
|
A:HIS72
|
2.9
|
32.5
|
1.0
|
C5N
|
A:NAP500
|
3.3
|
24.8
|
1.0
|
CB
|
A:CYS50
|
3.3
|
22.6
|
1.0
|
CD2
|
A:HIS72
|
3.4
|
28.4
|
1.0
|
CB
|
A:CYS166
|
3.6
|
24.9
|
1.0
|
OG
|
A:SER52
|
3.8
|
22.1
|
1.0
|
C6N
|
A:NAP500
|
3.9
|
23.1
|
1.0
|
CB
|
A:SER52
|
3.9
|
22.2
|
1.0
|
ND1
|
A:HIS72
|
4.0
|
31.1
|
1.0
|
C4N
|
A:NAP500
|
4.1
|
22.5
|
1.0
|
CG
|
A:HIS72
|
4.3
|
30.1
|
1.0
|
CA
|
A:CYS50
|
4.8
|
21.3
|
1.0
|
OE1
|
A:GLU73
|
4.8
|
30.0
|
1.0
|
CA
|
A:CYS166
|
4.9
|
23.1
|
1.0
|
N
|
A:SER52
|
5.0
|
22.5
|
1.0
|
|
Zinc binding site 2 out
of 4 in 1yqx
Go back to
Zinc Binding Sites List in 1yqx
Zinc binding site 2 out
of 4 in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2000
b:43.4
occ:1.00
|
SG
|
A:CYS103
|
2.4
|
46.8
|
1.0
|
SG
|
A:CYS109
|
2.4
|
40.7
|
1.0
|
SG
|
A:CYS117
|
2.5
|
34.8
|
1.0
|
SG
|
A:CYS106
|
2.7
|
60.2
|
1.0
|
CB
|
A:CYS117
|
3.2
|
36.1
|
1.0
|
CB
|
A:CYS103
|
3.4
|
47.3
|
1.0
|
N
|
A:HIS104
|
3.4
|
49.3
|
1.0
|
N
|
A:CYS103
|
3.6
|
46.2
|
1.0
|
CB
|
A:CYS106
|
3.7
|
56.6
|
1.0
|
CB
|
A:CYS109
|
3.7
|
44.7
|
1.0
|
CA
|
A:CYS103
|
3.8
|
47.2
|
1.0
|
N
|
A:CYS106
|
3.9
|
55.0
|
1.0
|
C
|
A:CYS103
|
4.0
|
48.1
|
1.0
|
N
|
A:SER105
|
4.1
|
54.0
|
1.0
|
CA
|
A:CYS117
|
4.2
|
36.6
|
1.0
|
N
|
A:CYS109
|
4.3
|
45.8
|
1.0
|
CA
|
A:HIS104
|
4.3
|
51.7
|
1.0
|
CA
|
A:CYS106
|
4.4
|
55.5
|
1.0
|
CB
|
A:ALA102
|
4.5
|
43.0
|
1.0
|
CA
|
A:CYS109
|
4.6
|
45.6
|
1.0
|
C
|
A:ALA102
|
4.7
|
45.6
|
1.0
|
C
|
A:HIS104
|
4.7
|
53.0
|
1.0
|
CD
|
A:PRO118
|
4.8
|
35.1
|
1.0
|
C
|
A:SER105
|
4.9
|
55.6
|
1.0
|
C
|
A:CYS106
|
5.0
|
54.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 1yqx
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Zinc Binding Sites List in 1yqx
Zinc binding site 3 out
of 4 in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn3000
b:32.9
occ:1.00
|
SG
|
B:CYS103
|
2.3
|
36.4
|
1.0
|
SG
|
B:CYS109
|
2.4
|
38.8
|
1.0
|
SG
|
B:CYS106
|
2.5
|
37.3
|
1.0
|
SG
|
B:CYS117
|
2.5
|
24.3
|
1.0
|
CB
|
B:CYS103
|
3.3
|
34.4
|
1.0
|
CB
|
B:CYS117
|
3.3
|
25.8
|
1.0
|
CB
|
B:CYS109
|
3.5
|
37.0
|
1.0
|
CB
|
B:CYS106
|
3.5
|
35.7
|
1.0
|
N
|
B:CYS103
|
3.8
|
33.5
|
1.0
|
N
|
B:HIS104
|
3.8
|
35.2
|
1.0
|
CA
|
B:CYS103
|
3.9
|
34.6
|
1.0
|
N
|
B:CYS106
|
4.1
|
37.1
|
1.0
|
C
|
B:CYS103
|
4.2
|
34.5
|
1.0
|
N
|
B:SER105
|
4.2
|
35.9
|
1.0
|
N
|
B:CYS109
|
4.2
|
35.5
|
1.0
|
CA
|
B:CYS117
|
4.2
|
28.6
|
1.0
|
OG
|
B:SER108
|
4.2
|
43.5
|
1.0
|
CA
|
B:CYS106
|
4.4
|
37.0
|
1.0
|
CA
|
B:CYS109
|
4.4
|
35.7
|
1.0
|
CD
|
B:PRO118
|
4.5
|
33.2
|
1.0
|
C
|
B:SER105
|
4.6
|
36.6
|
1.0
|
CA
|
B:HIS104
|
4.7
|
36.4
|
1.0
|
C
|
B:CYS106
|
4.9
|
37.4
|
1.0
|
CB
|
B:ALA102
|
4.9
|
31.0
|
1.0
|
C
|
B:ALA102
|
4.9
|
33.9
|
1.0
|
C
|
B:HIS104
|
5.0
|
35.3
|
1.0
|
O
|
B:CYS106
|
5.0
|
36.3
|
1.0
|
|
Zinc binding site 4 out
of 4 in 1yqx
Go back to
Zinc Binding Sites List in 1yqx
Zinc binding site 4 out
of 4 in the Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Sinapyl Alcohol Dehydrogenase at 2.5 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn4000
b:29.6
occ:1.00
|
NE2
|
B:HIS72
|
2.2
|
28.2
|
1.0
|
SG
|
B:CYS166
|
2.3
|
27.0
|
1.0
|
O
|
B:HOH4001
|
2.4
|
19.3
|
1.0
|
SG
|
B:CYS50
|
2.5
|
25.7
|
1.0
|
CE1
|
B:HIS72
|
2.8
|
29.4
|
1.0
|
CD2
|
B:HIS72
|
3.3
|
27.4
|
1.0
|
C5N
|
B:NAP600
|
3.3
|
28.9
|
1.0
|
CB
|
B:CYS50
|
3.3
|
25.6
|
1.0
|
CB
|
B:CYS166
|
3.5
|
25.7
|
1.0
|
ND1
|
B:HIS72
|
3.9
|
28.6
|
1.0
|
C6N
|
B:NAP600
|
4.0
|
26.7
|
1.0
|
CB
|
B:SER52
|
4.0
|
24.9
|
1.0
|
OG
|
B:SER52
|
4.1
|
25.6
|
1.0
|
C4N
|
B:NAP600
|
4.1
|
29.0
|
1.0
|
CG
|
B:HIS72
|
4.2
|
26.5
|
1.0
|
OE1
|
B:GLU73
|
4.7
|
27.0
|
1.0
|
CA
|
B:CYS50
|
4.8
|
24.7
|
1.0
|
CA
|
B:CYS166
|
4.9
|
25.8
|
1.0
|
SG
|
B:CYS98
|
4.9
|
43.7
|
1.0
|
|
Reference:
E.K.Bomati,
J.P.Noel.
Structural and Kinetic Basis For Substrate Selectivity in Populus Tremuloides Sinapyl Alcohol Dehydrogenase. Plant Cell V. 17 1598 2005.
ISSN: ISSN 1040-4651
PubMed: 15829607
DOI: 10.1105/TPC.104.029983
Page generated: Wed Oct 16 21:03:08 2024
|