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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:

Sodium (Na) 5 atoms

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

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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

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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

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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

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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

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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: Tue Oct 27 16:50:02 2020

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