Arsenic in PDB 3enz: Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion
Enzymatic activity of Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion
All present enzymatic activity of Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion:
2.4.2.1;
Protein crystallography data
The structure of Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion, PDB code: 3enz
was solved by
A.Chaikuad,
R.L.Brady,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
145.86 /
2.03
|
Space group
|
I 41 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
177.820,
177.820,
253.868,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16 /
19.3
|
Other elements in 3enz:
The structure of Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion also contains other interesting chemical elements:
Arsenic Binding Sites:
The binding sites of Arsenic atom in the Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion
(pdb code 3enz). This binding sites where shown within
5.0 Angstroms radius around Arsenic atom.
In total 6 binding sites of Arsenic where determined in the
Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion, PDB code: 3enz:
Jump to Arsenic binding site number:
1;
2;
3;
4;
5;
6;
Arsenic binding site 1 out
of 6 in 3enz
Go back to
Arsenic Binding Sites List in 3enz
Arsenic binding site 1 out
of 6 in the Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 1 of Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:As303
b:26.8
occ:1.00
|
AS
|
A:ART303
|
0.0
|
26.8
|
1.0
|
O2
|
A:ART303
|
1.9
|
23.9
|
1.0
|
O4
|
A:ART303
|
1.9
|
23.8
|
1.0
|
O1
|
A:ART303
|
1.9
|
22.8
|
1.0
|
O3
|
A:ART303
|
1.9
|
27.5
|
1.0
|
O4'
|
A:R1X302
|
3.5
|
27.5
|
0.8
|
C1'
|
A:R1X302
|
3.6
|
16.5
|
0.8
|
N
|
A:SER91
|
3.7
|
12.1
|
1.0
|
O3'
|
A:R1X302
|
3.7
|
19.3
|
0.8
|
NH1
|
A:ARG27
|
3.7
|
23.3
|
1.0
|
NH1
|
A:ARG88
|
3.8
|
7.4
|
1.0
|
OG
|
A:SER91
|
3.8
|
11.5
|
1.0
|
NH2
|
A:ARG27
|
3.8
|
23.1
|
1.0
|
CA
|
A:GLY23
|
3.9
|
15.3
|
1.0
|
NH2
|
B:ARG45
|
3.9
|
9.9
|
1.0
|
N
|
A:GLY23
|
4.0
|
15.1
|
1.0
|
NH1
|
B:ARG45
|
4.0
|
11.4
|
1.0
|
CA
|
A:GLY90
|
4.0
|
12.4
|
1.0
|
C4'
|
A:R1X302
|
4.1
|
23.3
|
0.8
|
NH2
|
A:ARG88
|
4.1
|
9.1
|
1.0
|
C3'
|
A:R1X302
|
4.2
|
24.6
|
0.8
|
C2'
|
A:R1X302
|
4.3
|
22.6
|
0.8
|
CZ
|
A:ARG27
|
4.3
|
25.9
|
1.0
|
C
|
A:GLY90
|
4.4
|
12.8
|
1.0
|
O2'
|
A:R1X302
|
4.4
|
16.4
|
0.8
|
CZ
|
A:ARG88
|
4.4
|
10.2
|
1.0
|
CZ
|
B:ARG45
|
4.5
|
15.7
|
1.0
|
N
|
A:ASP24
|
4.6
|
16.2
|
1.0
|
C
|
A:GLY23
|
4.7
|
16.4
|
1.0
|
CB
|
A:SER91
|
4.7
|
10.1
|
1.0
|
OE1
|
A:GLU184
|
4.7
|
14.5
|
1.0
|
O
|
A:SER91
|
4.7
|
11.7
|
1.0
|
CA
|
A:SER91
|
4.8
|
11.6
|
1.0
|
|
Arsenic binding site 2 out
of 6 in 3enz
Go back to
Arsenic Binding Sites List in 3enz
Arsenic binding site 2 out
of 6 in the Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 2 of Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:As303
b:27.0
occ:1.00
|
AS
|
B:ART303
|
0.0
|
27.0
|
1.0
|
O1
|
B:ART303
|
1.9
|
20.6
|
1.0
|
O4
|
B:ART303
|
1.9
|
20.8
|
1.0
|
O2
|
B:ART303
|
1.9
|
25.2
|
1.0
|
O3
|
B:ART303
|
1.9
|
25.7
|
1.0
|
O4'
|
B:R1X302
|
3.5
|
27.5
|
0.8
|
C1'
|
B:R1X302
|
3.5
|
16.5
|
0.8
|
N
|
B:SER91
|
3.7
|
9.2
|
1.0
|
OG
|
B:SER91
|
3.7
|
7.4
|
1.0
|
O3'
|
B:R1X302
|
3.8
|
19.3
|
0.8
|
NH1
|
B:ARG88
|
3.8
|
7.3
|
1.0
|
NH1
|
B:ARG27
|
3.9
|
23.2
|
1.0
|
NH2
|
A:ARG45
|
3.9
|
11.7
|
1.0
|
NH2
|
B:ARG27
|
3.9
|
21.8
|
1.0
|
CA
|
B:GLY23
|
4.0
|
15.0
|
1.0
|
N
|
B:GLY23
|
4.0
|
12.7
|
1.0
|
CA
|
B:GLY90
|
4.1
|
10.9
|
1.0
|
NH1
|
A:ARG45
|
4.1
|
9.8
|
1.0
|
C4'
|
B:R1X302
|
4.1
|
23.3
|
0.8
|
NH2
|
B:ARG88
|
4.1
|
8.8
|
1.0
|
C2'
|
B:R1X302
|
4.2
|
22.6
|
0.8
|
C3'
|
B:R1X302
|
4.2
|
24.6
|
0.8
|
C
|
B:GLY90
|
4.3
|
10.9
|
1.0
|
CZ
|
B:ARG27
|
4.4
|
24.9
|
1.0
|
O2'
|
B:R1X302
|
4.4
|
16.4
|
0.8
|
CZ
|
B:ARG88
|
4.5
|
9.4
|
1.0
|
CZ
|
A:ARG45
|
4.5
|
12.7
|
1.0
|
CB
|
B:SER91
|
4.6
|
9.1
|
1.0
|
CA
|
B:SER91
|
4.6
|
9.2
|
1.0
|
N
|
B:ASP24
|
4.7
|
15.6
|
1.0
|
OE1
|
B:GLU184
|
4.7
|
16.4
|
1.0
|
O
|
B:SER91
|
4.8
|
10.2
|
1.0
|
C
|
B:GLY23
|
4.8
|
15.6
|
1.0
|
|
Arsenic binding site 3 out
of 6 in 3enz
Go back to
Arsenic Binding Sites List in 3enz
Arsenic binding site 3 out
of 6 in the Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 3 of Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:As303
b:25.2
occ:1.00
|
AS
|
C:ART303
|
0.0
|
25.2
|
1.0
|
O2
|
C:ART303
|
1.9
|
23.4
|
1.0
|
O4
|
C:ART303
|
1.9
|
23.1
|
1.0
|
O1
|
C:ART303
|
1.9
|
21.9
|
1.0
|
O3
|
C:ART303
|
1.9
|
24.4
|
1.0
|
O4'
|
C:R1X302
|
3.4
|
25.4
|
0.8
|
C1'
|
C:R1X302
|
3.4
|
17.2
|
0.8
|
N
|
C:SER91
|
3.7
|
11.6
|
1.0
|
OG
|
C:SER91
|
3.7
|
11.2
|
1.0
|
O3'
|
C:R1X302
|
3.7
|
21.6
|
0.8
|
NH2
|
C:ARG27
|
3.8
|
16.2
|
1.0
|
NH1
|
C:ARG88
|
3.8
|
13.6
|
1.0
|
NH1
|
C:ARG27
|
3.8
|
13.1
|
1.0
|
CA
|
C:GLY23
|
3.9
|
10.8
|
1.0
|
N
|
C:GLY23
|
4.0
|
10.7
|
1.0
|
NH2
|
E:ARG45
|
4.0
|
15.1
|
1.0
|
NH1
|
E:ARG45
|
4.0
|
16.0
|
1.0
|
NH2
|
C:ARG88
|
4.1
|
11.0
|
1.0
|
CA
|
C:GLY90
|
4.1
|
11.1
|
1.0
|
C4'
|
C:R1X302
|
4.2
|
23.7
|
0.8
|
C2'
|
C:R1X302
|
4.2
|
24.4
|
0.8
|
CZ
|
C:ARG27
|
4.2
|
17.5
|
1.0
|
C3'
|
C:R1X302
|
4.3
|
24.3
|
0.8
|
C
|
C:GLY90
|
4.4
|
11.9
|
1.0
|
CZ
|
C:ARG88
|
4.4
|
13.4
|
1.0
|
O2'
|
C:R1X302
|
4.4
|
18.3
|
0.8
|
CZ
|
E:ARG45
|
4.5
|
17.9
|
1.0
|
CB
|
C:SER91
|
4.6
|
11.1
|
1.0
|
N
|
C:ASP24
|
4.6
|
10.9
|
1.0
|
CA
|
C:SER91
|
4.6
|
11.5
|
1.0
|
OE1
|
C:GLU184
|
4.7
|
15.3
|
1.0
|
C
|
C:GLY23
|
4.7
|
11.1
|
1.0
|
O
|
C:SER91
|
4.8
|
11.1
|
1.0
|
|
Arsenic binding site 4 out
of 6 in 3enz
Go back to
Arsenic Binding Sites List in 3enz
Arsenic binding site 4 out
of 6 in the Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 4 of Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:As303
b:31.8
occ:1.00
|
AS
|
D:ART303
|
0.0
|
31.8
|
1.0
|
O2
|
D:ART303
|
1.9
|
28.0
|
1.0
|
O4
|
D:ART303
|
1.9
|
28.0
|
1.0
|
O1
|
D:ART303
|
1.9
|
28.8
|
1.0
|
O3
|
D:ART303
|
1.9
|
31.0
|
1.0
|
C1'
|
D:R1X302
|
3.4
|
24.3
|
0.8
|
O4'
|
D:R1X302
|
3.6
|
30.7
|
0.8
|
N
|
D:SER91
|
3.7
|
10.6
|
1.0
|
O3'
|
D:R1X302
|
3.7
|
24.8
|
0.8
|
NH1
|
D:ARG88
|
3.7
|
11.7
|
1.0
|
NH1
|
D:ARG27
|
3.8
|
28.5
|
1.0
|
OG
|
D:SER91
|
3.8
|
9.5
|
1.0
|
NH2
|
D:ARG27
|
3.9
|
29.1
|
1.0
|
NH2
|
F:ARG45
|
3.9
|
21.0
|
1.0
|
N
|
D:GLY23
|
4.0
|
14.2
|
1.0
|
CA
|
D:GLY23
|
4.0
|
14.4
|
1.0
|
NH1
|
F:ARG45
|
4.0
|
20.2
|
1.0
|
CA
|
D:GLY90
|
4.0
|
11.8
|
1.0
|
NH2
|
D:ARG88
|
4.0
|
12.1
|
1.0
|
C2'
|
D:R1X302
|
4.2
|
28.6
|
0.8
|
C4'
|
D:R1X302
|
4.2
|
29.6
|
0.8
|
C3'
|
D:R1X302
|
4.3
|
28.9
|
0.8
|
CZ
|
D:ARG27
|
4.3
|
29.7
|
1.0
|
C
|
D:GLY90
|
4.3
|
11.5
|
1.0
|
CZ
|
D:ARG88
|
4.4
|
10.7
|
1.0
|
CZ
|
F:ARG45
|
4.4
|
21.4
|
1.0
|
O2'
|
D:R1X302
|
4.5
|
20.0
|
0.8
|
CB
|
D:SER91
|
4.6
|
10.5
|
1.0
|
CA
|
D:SER91
|
4.6
|
10.2
|
1.0
|
O
|
D:SER91
|
4.7
|
10.8
|
1.0
|
N
|
D:ASP24
|
4.7
|
16.4
|
1.0
|
OE1
|
D:GLU184
|
4.7
|
12.7
|
1.0
|
C
|
D:GLY23
|
4.8
|
16.2
|
1.0
|
|
Arsenic binding site 5 out
of 6 in 3enz
Go back to
Arsenic Binding Sites List in 3enz
Arsenic binding site 5 out
of 6 in the Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 5 of Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:As303
b:26.8
occ:1.00
|
AS
|
E:ART303
|
0.0
|
26.8
|
1.0
|
O4
|
E:ART303
|
1.9
|
23.4
|
1.0
|
O1
|
E:ART303
|
1.9
|
24.8
|
1.0
|
O3
|
E:ART303
|
1.9
|
26.4
|
1.0
|
O2
|
E:ART303
|
1.9
|
26.2
|
1.0
|
C1'
|
E:R1X302
|
3.3
|
24.3
|
0.8
|
O4'
|
E:R1X302
|
3.4
|
30.7
|
0.8
|
NH1
|
E:ARG27
|
3.6
|
26.2
|
1.0
|
OG
|
E:SER91
|
3.7
|
12.6
|
1.0
|
N
|
E:SER91
|
3.7
|
14.8
|
1.0
|
O3'
|
E:R1X302
|
3.7
|
24.8
|
0.8
|
NH1
|
E:ARG88
|
3.7
|
14.8
|
1.0
|
NH2
|
C:ARG45
|
3.8
|
14.0
|
1.0
|
NH2
|
E:ARG27
|
3.9
|
26.5
|
1.0
|
NH1
|
C:ARG45
|
4.0
|
11.7
|
1.0
|
CA
|
E:GLY23
|
4.0
|
18.6
|
1.0
|
N
|
E:GLY23
|
4.0
|
18.1
|
1.0
|
CA
|
E:GLY90
|
4.0
|
14.8
|
1.0
|
NH2
|
E:ARG88
|
4.1
|
14.6
|
1.0
|
C4'
|
E:R1X302
|
4.1
|
29.6
|
0.8
|
C2'
|
E:R1X302
|
4.2
|
28.6
|
0.8
|
C3'
|
E:R1X302
|
4.2
|
28.9
|
0.8
|
CZ
|
E:ARG27
|
4.2
|
28.4
|
1.0
|
C
|
E:GLY90
|
4.3
|
14.9
|
1.0
|
CZ
|
E:ARG88
|
4.4
|
13.2
|
1.0
|
CZ
|
C:ARG45
|
4.4
|
15.3
|
1.0
|
O2'
|
E:R1X302
|
4.5
|
20.0
|
0.8
|
CB
|
E:SER91
|
4.5
|
13.6
|
1.0
|
CA
|
E:SER91
|
4.6
|
14.4
|
1.0
|
OE1
|
E:GLU184
|
4.7
|
13.7
|
1.0
|
O
|
E:SER91
|
4.7
|
14.4
|
1.0
|
N
|
E:ASP24
|
4.7
|
19.9
|
1.0
|
C
|
E:GLY23
|
4.8
|
19.6
|
1.0
|
|
Arsenic binding site 6 out
of 6 in 3enz
Go back to
Arsenic Binding Sites List in 3enz
Arsenic binding site 6 out
of 6 in the Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 6 of Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:As303
b:36.6
occ:0.80
|
AS
|
F:ART303
|
0.0
|
36.6
|
0.8
|
O1
|
F:ART303
|
1.9
|
31.2
|
0.8
|
O4
|
F:ART303
|
1.9
|
34.4
|
0.8
|
O2
|
F:ART303
|
1.9
|
36.7
|
0.8
|
O3
|
F:ART303
|
2.0
|
36.0
|
0.8
|
C1'
|
F:R1X302
|
3.6
|
24.8
|
0.7
|
O4'
|
F:R1X302
|
3.6
|
29.2
|
0.7
|
NH1
|
F:ARG88
|
3.6
|
14.7
|
1.0
|
O3'
|
F:R1X302
|
3.8
|
27.4
|
0.7
|
NH2
|
D:ARG45
|
3.8
|
23.3
|
1.0
|
N
|
F:GLY23
|
3.8
|
15.4
|
1.0
|
CA
|
F:GLY23
|
3.8
|
15.9
|
1.0
|
N
|
F:SER91
|
3.8
|
14.9
|
1.0
|
CA
|
F:GLY90
|
3.9
|
16.4
|
1.0
|
NH2
|
F:ARG88
|
4.0
|
15.4
|
1.0
|
OG
|
F:SER91
|
4.1
|
15.9
|
1.0
|
NH1
|
D:ARG45
|
4.2
|
22.8
|
1.0
|
C4'
|
F:R1X302
|
4.2
|
26.2
|
0.7
|
C2'
|
F:R1X302
|
4.3
|
28.1
|
0.7
|
CZ
|
F:ARG88
|
4.3
|
14.9
|
1.0
|
O2'
|
F:R1X302
|
4.3
|
21.2
|
0.7
|
C3'
|
F:R1X302
|
4.3
|
28.2
|
0.7
|
C
|
F:GLY90
|
4.4
|
15.8
|
1.0
|
CZ
|
D:ARG45
|
4.5
|
21.8
|
1.0
|
OE1
|
F:GLU184
|
4.7
|
19.6
|
1.0
|
C
|
F:GLY23
|
4.8
|
16.4
|
1.0
|
N
|
F:ASP24
|
4.8
|
16.2
|
1.0
|
CA
|
F:SER91
|
4.9
|
14.9
|
1.0
|
CB
|
F:SER91
|
4.9
|
15.0
|
1.0
|
O
|
F:SER91
|
4.9
|
14.0
|
1.0
|
|
Reference:
A.Chaikuad,
R.L.Brady.
Conservation of Structure and Activity in Plasmodium Purine Nucleoside Phosphorylases. Bmc Struct.Biol. V. 9 42 2009.
ISSN: ESSN 1472-6807
PubMed: 19575810
DOI: 10.1186/1472-6807-9-42
Page generated: Wed Jul 10 11:38:52 2024
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