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Sodium 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 (As) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Arsenolytic Structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase with Hypoxanthine, Ribose and Arsenate Ion, PDB code: 3enz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3enz

Go back to Sodium Binding Sites List in 3enz
Sodium binding site 1 out of 5 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 Sodium with other atoms in the Na 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:Na311

b:12.3
occ:1.00
 O A:HOH353 2.6 31.0 1.0
O B:HOH408 2.6 25.9 1.0
OE1 B:GLU46 2.6 12.7 1.0
O B:VAL66 2.7 11.7 1.0
O A:VAL66 2.7 11.0 1.0
OE1 A:GLU46 2.9 13.0 1.0
N A:VAL66 3.6 11.6 1.0
O A:HOH399 3.6 16.4 1.0
N B:VAL66 3.6 12.1 1.0
CD B:GLU46 3.7 13.8 1.0
C B:VAL66 3.7 11.9 1.0
C A:VAL66 3.7 11.0 1.0
CD A:GLU46 3.9 13.8 1.0
C B:GLY65 4.1 12.6 1.0
CA B:GLY65 4.1 13.1 1.0
C A:GLY65 4.1 12.5 1.0
CA A:VAL66 4.1 10.9 1.0
CA B:VAL66 4.2 11.5 1.0
CA A:GLY65 4.2 12.4 1.0
CG B:GLU46 4.3 15.1 1.0
CA A:GLY70 4.4 11.2 1.0
CA B:GLY70 4.4 11.8 1.0
CG A:GLU46 4.5 16.2 1.0
CB A:VAL66 4.6 11.7 1.0
CB B:VAL66 4.6 11.7 1.0
OE2 B:GLU46 4.7 15.1 1.0
O B:HIS64 4.8 13.2 1.0
N A:GLY67 4.9 11.1 1.0
N B:GLY67 4.9 11.8 1.0
OE2 A:GLU46 4.9 13.7 1.0
O A:HIS64 4.9 12.7 1.0
O B:GLY65 5.0 13.7 1.0

Sodium binding site 2 out of 5 in 3enz

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Sodium binding site 2 out of 5 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 Sodium with other atoms in the Na 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:Na306

b:54.6
occ:1.00
 O1 D:FMT304 2.2 40.5 1.0
ND2 B:ASN109 2.5 28.1 1.0
O D:HOH368 2.7 34.1 1.0
O D:GLY130 2.9 11.4 1.0
C D:FMT304 3.3 37.8 1.0
CG B:ASN109 3.4 20.1 1.0
OD1 B:ASN109 3.6 27.4 1.0
C D:GLY130 3.8 12.1 1.0
CA D:ASP131 3.9 12.8 1.0
N D:PHE132 4.0 13.3 1.0
N D:ASP131 4.2 12.5 1.0
O2 D:FMT304 4.4 35.1 1.0
CG2 D:VAL129 4.4 9.6 1.0
C D:ASP131 4.4 13.3 1.0
CG1 D:VAL129 4.6 10.1 1.0
CB B:ASN109 4.6 14.2 1.0
CZ B:PHE132 4.9 16.2 1.0
OD2 D:ASP131 4.9 14.4 1.0
CB D:ASP131 5.0 12.5 1.0

Sodium binding site 3 out of 5 in 3enz

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Sodium binding site 3 out of 5 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 Sodium with other atoms in the Na 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:Na310

b:12.8
occ:1.00
 OE1 E:GLU46 2.5 20.9 1.0
O C:HOH358 2.6 28.5 1.0
O E:HOH380 2.6 24.4 1.0
O E:VAL66 2.7 17.8 1.0
O C:VAL66 2.8 10.4 1.0
OE1 C:GLU46 2.8 10.1 1.0
N E:VAL66 3.5 17.3 1.0
N C:VAL66 3.6 10.0 1.0
O E:HOH323 3.6 15.0 1.0
CD E:GLU46 3.7 23.0 1.0
C E:VAL66 3.7 17.1 1.0
C C:VAL66 3.7 9.9 1.0
CD C:GLU46 3.8 11.9 1.0
C E:GLY65 4.0 17.9 1.0
C C:GLY65 4.1 9.9 1.0
CA E:VAL66 4.1 16.7 1.0
CA C:GLY65 4.1 9.4 1.0
CA E:GLY65 4.1 18.2 1.0
CA C:VAL66 4.2 9.7 1.0
CG E:GLU46 4.3 20.8 1.0
CG C:GLU46 4.4 12.6 1.0
CA C:GLY70 4.4 9.9 1.0
CA E:GLY70 4.5 16.9 1.0
OE2 E:GLU46 4.6 27.9 1.0
CB E:VAL66 4.6 17.2 1.0
CB C:VAL66 4.7 9.6 1.0
OE2 C:GLU46 4.7 12.5 1.0
N E:GLY67 4.8 16.7 1.0
O E:HIS64 4.8 17.8 1.0
N C:GLY67 4.8 9.4 1.0
O C:HIS64 4.9 10.8 1.0
O E:GLY65 4.9 18.5 1.0
O C:GLY65 4.9 10.3 1.0

Sodium binding site 4 out of 5 in 3enz

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Sodium binding site 4 out of 5 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 Sodium with other atoms in the Na 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:Na309

b:12.8
occ:1.00
 O D:HOH323 2.5 21.4 1.0
O F:HOH379 2.5 32.4 1.0
OE1 D:GLU46 2.7 19.3 1.0
O D:VAL66 2.7 13.1 1.0
O F:VAL66 2.8 16.0 1.0
OE1 F:GLU46 2.9 18.0 1.0
N D:VAL66 3.6 11.5 1.0
N F:VAL66 3.6 15.1 1.0
O F:HOH328 3.6 13.9 1.0
C D:VAL66 3.7 12.1 1.0
C F:VAL66 3.7 15.1 1.0
CD D:GLU46 3.8 17.6 1.0
CD F:GLU46 4.0 18.5 1.0
C D:GLY65 4.0 12.4 1.0
CA D:GLY65 4.1 11.8 1.0
CA D:VAL66 4.1 11.3 1.0
CA F:GLY65 4.1 14.8 1.0
C F:GLY65 4.1 15.0 1.0
CA F:VAL66 4.2 14.5 1.0
CG D:GLU46 4.4 15.6 1.0
CA F:GLY70 4.4 13.5 1.0
CA D:GLY70 4.4 10.6 1.0
CB F:VAL66 4.6 14.3 1.0
CG F:GLU46 4.6 18.5 1.0
CB D:VAL66 4.6 11.1 1.0
OE2 D:GLU46 4.8 17.7 1.0
O D:HIS64 4.8 13.6 1.0
N D:GLY67 4.8 11.8 1.0
N F:GLY67 4.9 14.4 1.0
O D:GLY65 4.9 12.1 1.0
O F:HIS64 4.9 15.6 1.0
OE2 F:GLU46 5.0 19.6 1.0

Sodium binding site 5 out of 5 in 3enz

Go back to Sodium Binding Sites List in 3enz
Sodium binding site 5 out of 5 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 Sodium with other atoms in the Na 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
D:Na310

b:46.3
occ:1.00
 O1 D:FMT305 2.4 46.9 1.0
C D:FMT305 2.6 47.1 1.0
O2 D:FMT305 2.8 46.3 1.0
O D:ARG45 2.8 15.1 1.0
O F:HOH343 3.5 22.4 1.0
OH F:TYR43 3.6 19.2 1.0
O F:HOH349 3.6 23.1 1.0
N D:ARG45 3.7 13.9 1.0
CZ D:TYR43 3.7 18.3 1.0
CE2 D:TYR43 3.8 16.8 1.0
C D:ARG45 3.8 14.7 1.0
CG F:PRO25 3.9 16.9 1.0
CA D:ARG45 4.0 14.5 1.0
CE1 D:TYR43 4.0 18.1 1.0
CD2 D:TYR43 4.1 16.3 1.0
OH D:TYR43 4.2 15.5 1.0
CD1 D:TYR43 4.3 17.3 1.0
CG D:TYR43 4.4 17.2 1.0
C D:ASN44 4.4 15.0 1.0
CB F:PRO25 4.7 17.7 1.0
O D:TYR43 4.7 16.7 1.0
CA D:ASN44 4.7 15.6 1.0
OD1 F:ASP24 4.7 13.1 1.0
N F:GLY26 4.8 16.6 1.0
N D:ASN44 4.8 16.0 1.0
C D:TYR43 4.8 16.8 1.0
CZ F:TYR43 4.9 18.9 1.0
N D:GLU46 5.0 14.4 1.0
CD F:PRO25 5.0 16.2 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: Mon Oct 7 08:52:19 2024

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