Zinc in PDB 1yqd: Sinapyl Alcohol Dehydrogenase Complexed with Nadp+
Enzymatic activity of Sinapyl Alcohol Dehydrogenase Complexed with Nadp+
All present enzymatic activity of Sinapyl Alcohol Dehydrogenase Complexed with Nadp+:
1.1.1.195;
Protein crystallography data
The structure of Sinapyl Alcohol Dehydrogenase Complexed with Nadp+, PDB code: 1yqd
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)
|
38.32 /
1.65
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.477,
137.796,
69.523,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.5 /
21.3
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Sinapyl Alcohol Dehydrogenase Complexed with Nadp+
(pdb code 1yqd). 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 Complexed with Nadp+, PDB code: 1yqd:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 1yqd
Go back to
Zinc Binding Sites List in 1yqd
Zinc binding site 1 out
of 4 in the Sinapyl Alcohol Dehydrogenase Complexed with Nadp+
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 Complexed with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1000
b:13.3
occ:1.00
|
O
|
A:HOH2046
|
2.1
|
12.6
|
1.0
|
NE2
|
A:HIS72
|
2.2
|
11.9
|
1.0
|
SG
|
A:CYS166
|
2.3
|
14.0
|
1.0
|
SG
|
A:CYS50
|
2.4
|
11.0
|
1.0
|
CE1
|
A:HIS72
|
3.0
|
13.3
|
1.0
|
CD2
|
A:HIS72
|
3.2
|
11.3
|
1.0
|
CB
|
A:CYS50
|
3.2
|
10.5
|
1.0
|
C5N
|
A:NAP500
|
3.3
|
15.1
|
1.0
|
CB
|
A:CYS166
|
3.5
|
12.3
|
1.0
|
OG
|
A:SER52
|
3.6
|
11.4
|
1.0
|
CB
|
A:SER52
|
3.7
|
9.8
|
1.0
|
C6N
|
A:NAP500
|
3.9
|
13.8
|
1.0
|
SG
|
A:CYS98
|
4.0
|
15.5
|
1.0
|
O2
|
A:DTT700
|
4.1
|
20.2
|
1.0
|
ND1
|
A:HIS72
|
4.1
|
12.3
|
1.0
|
C4N
|
A:NAP500
|
4.2
|
15.5
|
1.0
|
CG
|
A:HIS72
|
4.2
|
10.3
|
1.0
|
O3
|
A:DTT700
|
4.4
|
18.5
|
1.0
|
OE1
|
A:GLU73
|
4.7
|
13.9
|
1.0
|
CA
|
A:CYS50
|
4.7
|
10.5
|
1.0
|
NH2
|
A:ARG348
|
4.9
|
9.8
|
1.0
|
CA
|
A:CYS166
|
4.9
|
10.5
|
1.0
|
N
|
A:SER52
|
4.9
|
9.9
|
1.0
|
S1
|
A:DTT700
|
4.9
|
30.5
|
1.0
|
CA
|
A:SER52
|
4.9
|
9.4
|
1.0
|
|
Zinc binding site 2 out
of 4 in 1yqd
Go back to
Zinc Binding Sites List in 1yqd
Zinc binding site 2 out
of 4 in the Sinapyl Alcohol Dehydrogenase Complexed with Nadp+
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 Complexed with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2000
b:17.2
occ:1.00
|
SG
|
A:CYS117
|
2.4
|
14.9
|
1.0
|
SG
|
A:CYS106
|
2.4
|
17.7
|
1.0
|
SG
|
A:CYS103
|
2.4
|
17.4
|
1.0
|
SG
|
A:CYS109
|
2.4
|
16.2
|
1.0
|
CB
|
A:CYS117
|
3.2
|
13.7
|
1.0
|
CB
|
A:CYS106
|
3.4
|
19.1
|
1.0
|
CB
|
A:CYS103
|
3.5
|
17.5
|
1.0
|
CB
|
A:CYS109
|
3.5
|
15.3
|
1.0
|
N
|
A:CYS103
|
3.7
|
14.9
|
1.0
|
N
|
A:HIS104
|
3.8
|
18.7
|
1.0
|
N
|
A:CYS106
|
3.9
|
20.6
|
1.0
|
CA
|
A:CYS103
|
4.0
|
16.8
|
1.0
|
N
|
A:CYS109
|
4.1
|
15.6
|
1.0
|
CA
|
A:CYS117
|
4.1
|
13.8
|
1.0
|
CA
|
A:CYS106
|
4.2
|
19.7
|
1.0
|
C
|
A:CYS103
|
4.3
|
18.6
|
1.0
|
N
|
A:SER105
|
4.3
|
23.1
|
1.0
|
CA
|
A:CYS109
|
4.4
|
15.1
|
1.0
|
CD
|
A:PRO118
|
4.6
|
16.8
|
1.0
|
CB
|
A:ALA102
|
4.7
|
13.1
|
1.0
|
CA
|
A:HIS104
|
4.7
|
20.7
|
1.0
|
C
|
A:CYS106
|
4.8
|
20.3
|
1.0
|
O
|
A:CYS106
|
4.8
|
18.9
|
1.0
|
C
|
A:ALA102
|
4.9
|
14.2
|
1.0
|
C
|
A:SER105
|
4.9
|
24.4
|
1.0
|
C
|
A:CYS117
|
5.0
|
15.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 1yqd
Go back to
Zinc Binding Sites List in 1yqd
Zinc binding site 3 out
of 4 in the Sinapyl Alcohol Dehydrogenase Complexed with Nadp+
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 Complexed with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn3000
b:17.1
occ:1.00
|
SG
|
B:CYS106
|
2.3
|
17.5
|
1.0
|
SG
|
B:CYS103
|
2.4
|
16.9
|
1.0
|
SG
|
B:CYS117
|
2.4
|
15.6
|
1.0
|
SG
|
B:CYS109
|
2.4
|
15.8
|
1.0
|
CB
|
B:CYS117
|
3.2
|
15.0
|
1.0
|
CB
|
B:CYS106
|
3.4
|
19.1
|
1.0
|
CB
|
B:CYS103
|
3.5
|
15.7
|
1.0
|
CB
|
B:CYS109
|
3.5
|
15.4
|
1.0
|
N
|
B:HIS104
|
3.7
|
17.1
|
1.0
|
N
|
B:CYS103
|
3.7
|
13.9
|
1.0
|
N
|
B:CYS106
|
3.9
|
20.6
|
1.0
|
CA
|
B:CYS103
|
4.0
|
15.8
|
1.0
|
N
|
B:CYS109
|
4.1
|
15.7
|
1.0
|
CA
|
B:CYS117
|
4.2
|
14.8
|
1.0
|
CA
|
B:CYS106
|
4.2
|
19.5
|
1.0
|
C
|
B:CYS103
|
4.2
|
18.0
|
1.0
|
N
|
B:SER105
|
4.3
|
20.2
|
1.0
|
CA
|
B:CYS109
|
4.4
|
15.5
|
1.0
|
CA
|
B:HIS104
|
4.6
|
19.8
|
1.0
|
CB
|
B:ALA102
|
4.7
|
12.6
|
1.0
|
CD
|
B:PRO118
|
4.7
|
17.4
|
1.0
|
C
|
B:CYS106
|
4.8
|
19.9
|
1.0
|
C
|
B:ALA102
|
4.8
|
13.8
|
1.0
|
O
|
B:CYS106
|
4.9
|
18.8
|
1.0
|
C
|
B:SER105
|
4.9
|
21.5
|
1.0
|
|
Zinc binding site 4 out
of 4 in 1yqd
Go back to
Zinc Binding Sites List in 1yqd
Zinc binding site 4 out
of 4 in the Sinapyl Alcohol Dehydrogenase Complexed with Nadp+
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 Complexed with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn4000
b:14.9
occ:1.00
|
O
|
B:HOH4083
|
2.1
|
12.9
|
1.0
|
NE2
|
B:HIS72
|
2.2
|
13.2
|
1.0
|
SG
|
B:CYS166
|
2.3
|
12.8
|
1.0
|
SG
|
B:CYS50
|
2.4
|
11.4
|
1.0
|
CE1
|
B:HIS72
|
2.9
|
13.6
|
1.0
|
CB
|
B:CYS50
|
3.2
|
11.4
|
1.0
|
CD2
|
B:HIS72
|
3.3
|
12.7
|
1.0
|
C5N
|
B:NAP600
|
3.3
|
15.0
|
1.0
|
CB
|
B:CYS166
|
3.5
|
12.6
|
1.0
|
OG
|
B:SER52
|
3.6
|
13.6
|
1.0
|
CB
|
B:SER52
|
3.8
|
11.9
|
1.0
|
C6N
|
B:NAP600
|
3.9
|
14.8
|
1.0
|
O2
|
B:DTT800
|
4.0
|
24.2
|
1.0
|
SG
|
B:CYS98
|
4.0
|
14.4
|
1.0
|
ND1
|
B:HIS72
|
4.1
|
13.9
|
1.0
|
C4N
|
B:NAP600
|
4.2
|
15.7
|
1.0
|
CG
|
B:HIS72
|
4.2
|
12.1
|
1.0
|
O3
|
B:DTT800
|
4.4
|
22.3
|
1.0
|
CA
|
B:CYS50
|
4.7
|
11.4
|
1.0
|
OE1
|
B:GLU73
|
4.7
|
13.8
|
1.0
|
S1
|
B:DTT800
|
4.9
|
31.6
|
1.0
|
CA
|
B:CYS166
|
4.9
|
11.5
|
1.0
|
N
|
B:SER52
|
4.9
|
10.7
|
1.0
|
NH2
|
B:ARG348
|
4.9
|
10.5
|
1.0
|
CA
|
B:SER52
|
5.0
|
11.9
|
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 21:02:48 2024
|