Phosphorus in PDB 1ahz: Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol
Enzymatic activity of Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol
All present enzymatic activity of Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol:
1.1.3.13;
Protein crystallography data
The structure of Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol, PDB code: 1ahz
was solved by
A.Mattevi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
3.30
|
Space group
|
I 4
|
Cell size a, b, c (Å), α, β, γ (°)
|
140.970,
140.970,
133.450,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.4 /
26.8
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol
(pdb code 1ahz). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 4 binding sites of Phosphorus where determined in the
Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol, PDB code: 1ahz:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
Phosphorus binding site 1 out
of 4 in 1ahz
Go back to
Phosphorus Binding Sites List in 1ahz
Phosphorus binding site 1 out
of 4 in the Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P600
b:23.1
occ:1.00
|
PA
|
A:FAD600
|
0.0
|
23.1
|
1.0
|
O1A
|
A:FAD600
|
1.5
|
30.2
|
1.0
|
O2A
|
A:FAD600
|
1.5
|
20.9
|
1.0
|
O5B
|
A:FAD600
|
1.6
|
21.4
|
1.0
|
O3P
|
A:FAD600
|
1.6
|
17.4
|
1.0
|
C5B
|
A:FAD600
|
2.6
|
18.7
|
1.0
|
P
|
A:FAD600
|
2.9
|
18.8
|
1.0
|
O2P
|
A:FAD600
|
3.2
|
18.1
|
1.0
|
O5'
|
A:FAD600
|
3.6
|
15.6
|
1.0
|
N
|
A:GLY103
|
3.6
|
14.3
|
1.0
|
C4B
|
A:FAD600
|
3.9
|
18.1
|
1.0
|
N
|
A:ILE102
|
4.0
|
7.7
|
1.0
|
CB
|
A:ASN105
|
4.0
|
18.7
|
1.0
|
O1P
|
A:FAD600
|
4.1
|
18.9
|
1.0
|
N
|
A:ASN105
|
4.2
|
12.6
|
1.0
|
N
|
A:ARG104
|
4.2
|
8.4
|
1.0
|
CA
|
A:GLY103
|
4.3
|
12.6
|
1.0
|
N
|
A:SER101
|
4.4
|
15.5
|
1.0
|
C3B
|
A:FAD600
|
4.4
|
22.7
|
1.0
|
CA
|
A:ILE102
|
4.5
|
5.3
|
1.0
|
C
|
A:GLY103
|
4.5
|
16.8
|
1.0
|
C8A
|
A:FAD600
|
4.5
|
15.8
|
1.0
|
C
|
A:ILE102
|
4.6
|
15.4
|
1.0
|
C5'
|
A:FAD600
|
4.6
|
13.3
|
1.0
|
CA
|
A:ASN105
|
4.7
|
14.3
|
1.0
|
CB
|
A:ILE100
|
4.8
|
6.0
|
1.0
|
CB
|
A:ILE102
|
4.8
|
12.4
|
1.0
|
CA
|
A:ARG104
|
4.9
|
8.8
|
1.0
|
O4B
|
A:FAD600
|
4.9
|
17.6
|
1.0
|
CG
|
A:ASN105
|
5.0
|
38.0
|
1.0
|
C
|
A:ARG104
|
5.0
|
16.7
|
1.0
|
|
Phosphorus binding site 2 out
of 4 in 1ahz
Go back to
Phosphorus Binding Sites List in 1ahz
Phosphorus binding site 2 out
of 4 in the Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P600
b:18.8
occ:1.00
|
P
|
A:FAD600
|
0.0
|
18.8
|
1.0
|
O2P
|
A:FAD600
|
1.5
|
18.1
|
1.0
|
O1P
|
A:FAD600
|
1.5
|
18.9
|
1.0
|
O5'
|
A:FAD600
|
1.6
|
15.6
|
1.0
|
O3P
|
A:FAD600
|
1.6
|
17.4
|
1.0
|
C5'
|
A:FAD600
|
2.6
|
13.3
|
1.0
|
PA
|
A:FAD600
|
2.9
|
23.1
|
1.0
|
O1A
|
A:FAD600
|
3.2
|
30.2
|
1.0
|
C4'
|
A:FAD600
|
3.3
|
12.0
|
1.0
|
O4'
|
A:FAD600
|
3.4
|
8.8
|
1.0
|
O2A
|
A:FAD600
|
3.7
|
20.9
|
1.0
|
N
|
A:SER175
|
3.7
|
6.8
|
1.0
|
N
|
A:ASN105
|
3.9
|
12.6
|
1.0
|
CA
|
A:ARG104
|
4.0
|
8.8
|
1.0
|
C
|
A:ARG104
|
4.0
|
16.7
|
1.0
|
O5B
|
A:FAD600
|
4.0
|
21.4
|
1.0
|
N
|
A:ARG104
|
4.1
|
8.4
|
1.0
|
CA
|
A:GLY174
|
4.2
|
20.0
|
1.0
|
CB
|
A:ILE102
|
4.3
|
12.4
|
1.0
|
CB
|
A:ARG104
|
4.3
|
8.4
|
1.0
|
CB
|
A:SER175
|
4.4
|
9.4
|
1.0
|
C
|
A:GLY174
|
4.5
|
15.5
|
1.0
|
CB
|
A:ASN105
|
4.5
|
18.7
|
1.0
|
CA
|
A:ASN105
|
4.5
|
14.3
|
1.0
|
C5B
|
A:FAD600
|
4.6
|
18.7
|
1.0
|
CA
|
A:SER175
|
4.6
|
4.2
|
1.0
|
O
|
A:ARG104
|
4.7
|
19.4
|
1.0
|
N
|
A:ASN179
|
4.7
|
2.3
|
1.0
|
CG2
|
A:ILE102
|
4.8
|
17.0
|
1.0
|
N
|
A:GLY103
|
4.8
|
14.3
|
1.0
|
C3'
|
A:FAD600
|
4.8
|
17.8
|
1.0
|
C
|
A:GLY178
|
4.8
|
3.6
|
1.0
|
O
|
A:SER175
|
4.8
|
2.2
|
1.0
|
CA
|
A:ILE102
|
4.9
|
5.3
|
1.0
|
CA
|
A:GLY178
|
4.9
|
2.7
|
1.0
|
N
|
A:ILE102
|
4.9
|
7.7
|
1.0
|
|
Phosphorus binding site 3 out
of 4 in 1ahz
Go back to
Phosphorus Binding Sites List in 1ahz
Phosphorus binding site 3 out
of 4 in the Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P600
b:23.1
occ:1.00
|
PA
|
B:FAD600
|
0.0
|
23.1
|
1.0
|
O1A
|
B:FAD600
|
1.5
|
30.2
|
1.0
|
O2A
|
B:FAD600
|
1.5
|
20.9
|
1.0
|
O5B
|
B:FAD600
|
1.6
|
21.4
|
1.0
|
O3P
|
B:FAD600
|
1.6
|
17.4
|
1.0
|
C5B
|
B:FAD600
|
2.6
|
18.7
|
1.0
|
P
|
B:FAD600
|
2.9
|
18.8
|
1.0
|
O2P
|
B:FAD600
|
3.2
|
18.1
|
1.0
|
O5'
|
B:FAD600
|
3.6
|
15.6
|
1.0
|
N
|
B:GLY103
|
3.6
|
14.3
|
1.0
|
C4B
|
B:FAD600
|
3.9
|
18.1
|
1.0
|
N
|
B:ILE102
|
4.0
|
7.7
|
1.0
|
CB
|
B:ASN105
|
4.0
|
18.7
|
1.0
|
O1P
|
B:FAD600
|
4.1
|
18.9
|
1.0
|
N
|
B:ASN105
|
4.2
|
12.6
|
1.0
|
N
|
B:ARG104
|
4.2
|
8.4
|
1.0
|
CA
|
B:GLY103
|
4.3
|
12.6
|
1.0
|
N
|
B:SER101
|
4.4
|
15.5
|
1.0
|
C3B
|
B:FAD600
|
4.4
|
22.7
|
1.0
|
CA
|
B:ILE102
|
4.5
|
5.3
|
1.0
|
C
|
B:GLY103
|
4.5
|
16.8
|
1.0
|
C8A
|
B:FAD600
|
4.5
|
15.8
|
1.0
|
C
|
B:ILE102
|
4.6
|
15.4
|
1.0
|
C5'
|
B:FAD600
|
4.6
|
13.3
|
1.0
|
CA
|
B:ASN105
|
4.7
|
14.3
|
1.0
|
CB
|
B:ILE100
|
4.8
|
6.0
|
1.0
|
CB
|
B:ILE102
|
4.8
|
12.4
|
1.0
|
CA
|
B:ARG104
|
4.9
|
8.8
|
1.0
|
O4B
|
B:FAD600
|
4.9
|
17.6
|
1.0
|
CG
|
B:ASN105
|
5.0
|
38.0
|
1.0
|
C
|
B:ARG104
|
5.0
|
16.7
|
1.0
|
|
Phosphorus binding site 4 out
of 4 in 1ahz
Go back to
Phosphorus Binding Sites List in 1ahz
Phosphorus binding site 4 out
of 4 in the Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Structure of the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase in Complex with 4-(1-Heptenyl)Phenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P600
b:18.8
occ:1.00
|
P
|
B:FAD600
|
0.0
|
18.8
|
1.0
|
O2P
|
B:FAD600
|
1.5
|
18.1
|
1.0
|
O1P
|
B:FAD600
|
1.5
|
18.9
|
1.0
|
O5'
|
B:FAD600
|
1.6
|
15.6
|
1.0
|
O3P
|
B:FAD600
|
1.6
|
17.4
|
1.0
|
C5'
|
B:FAD600
|
2.6
|
13.3
|
1.0
|
PA
|
B:FAD600
|
2.9
|
23.1
|
1.0
|
O1A
|
B:FAD600
|
3.2
|
30.2
|
1.0
|
C4'
|
B:FAD600
|
3.3
|
12.0
|
1.0
|
O4'
|
B:FAD600
|
3.4
|
8.8
|
1.0
|
O2A
|
B:FAD600
|
3.7
|
20.9
|
1.0
|
N
|
B:SER175
|
3.7
|
6.8
|
1.0
|
N
|
B:ASN105
|
3.9
|
12.6
|
1.0
|
CA
|
B:ARG104
|
4.0
|
8.8
|
1.0
|
C
|
B:ARG104
|
4.0
|
16.7
|
1.0
|
O5B
|
B:FAD600
|
4.0
|
21.4
|
1.0
|
N
|
B:ARG104
|
4.1
|
8.4
|
1.0
|
CA
|
B:GLY174
|
4.2
|
20.0
|
1.0
|
CB
|
B:ILE102
|
4.3
|
12.4
|
1.0
|
CB
|
B:ARG104
|
4.3
|
8.4
|
1.0
|
CB
|
B:SER175
|
4.3
|
9.4
|
1.0
|
C
|
B:GLY174
|
4.5
|
15.5
|
1.0
|
CB
|
B:ASN105
|
4.5
|
18.7
|
1.0
|
CA
|
B:ASN105
|
4.5
|
14.3
|
1.0
|
C5B
|
B:FAD600
|
4.6
|
18.7
|
1.0
|
CA
|
B:SER175
|
4.6
|
4.2
|
1.0
|
O
|
B:ARG104
|
4.7
|
19.4
|
1.0
|
N
|
B:ASN179
|
4.7
|
2.3
|
1.0
|
CG2
|
B:ILE102
|
4.8
|
17.0
|
1.0
|
N
|
B:GLY103
|
4.8
|
14.3
|
1.0
|
C3'
|
B:FAD600
|
4.8
|
17.8
|
1.0
|
C
|
B:GLY178
|
4.8
|
3.6
|
1.0
|
O
|
B:SER175
|
4.8
|
2.2
|
1.0
|
CA
|
B:ILE102
|
4.9
|
5.3
|
1.0
|
CA
|
B:GLY178
|
4.9
|
2.7
|
1.0
|
N
|
B:ILE102
|
4.9
|
7.7
|
1.0
|
|
Reference:
A.Mattevi,
M.W.Fraaije,
A.Mozzarelli,
L.Olivi,
A.Coda,
W.J.Van Berkel.
Crystal Structures and Inhibitor Binding in the Octameric Flavoenzyme Vanillyl-Alcohol Oxidase: the Shape of the Active-Site Cavity Controls Substrate Specificity. Structure V. 5 907 1997.
ISSN: ISSN 0969-2126
PubMed: 9261083
DOI: 10.1016/S0969-2126(97)00245-1
Page generated: Fri Sep 25 12:58:20 2020
|