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Sodium in PDB 6vsu: Arginase From Arabidopsis Thaliana in Complex with Ornithine

Enzymatic activity of Arginase From Arabidopsis Thaliana in Complex with Ornithine

All present enzymatic activity of Arginase From Arabidopsis Thaliana in Complex with Ornithine:
3.5.3.1; 3.5.3.11;

Protein crystallography data

The structure of Arginase From Arabidopsis Thaliana in Complex with Ornithine, PDB code: 6vsu was solved by B.Sekula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.97 / 2.25
Space group I 41 1
Cell size a, b, c (Å), α, β, γ (°) 267.322, 267.322, 262.894, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.7

Other elements in 6vsu:

The structure of Arginase From Arabidopsis Thaliana in Complex with Ornithine also contains other interesting chemical elements:

Manganese (Mn) 48 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Sodium atom in the Arginase From Arabidopsis Thaliana in Complex with Ornithine (pdb code 6vsu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 24 binding sites of Sodium where determined in the Arginase From Arabidopsis Thaliana in Complex with Ornithine, PDB code: 6vsu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 24 in 6vsu

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Sodium binding site 1 out of 24 in the Arginase From Arabidopsis Thaliana in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Arginase From Arabidopsis Thaliana in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:34.4
occ:1.00
 O A:HOH586 2.6 26.1 1.0
OE1 A:GLU313 2.7 32.7 1.0
OG A:SER76 2.9 33.5 1.0
O A:LEU79 2.9 29.3 1.0
OG A:SER283 3.0 30.4 1.0
CB A:SER76 3.3 33.4 1.0
CB A:SER283 3.4 28.9 1.0
CG A:PRO82 3.7 42.0 1.0
CD A:GLU313 3.7 33.1 1.0
O A:HOH523 3.7 30.1 1.0
CE1 A:HIS201 3.8 47.6 1.0
ND1 A:HIS201 3.9 47.0 1.0
OE2 A:GLU313 3.9 35.7 1.0
CD A:PRO82 4.0 42.9 1.0
C A:LEU79 4.1 30.1 1.0
CA A:SER76 4.3 34.6 1.0
NE2 A:HIS284 4.5 32.1 1.0
CB A:ASP160 4.6 37.2 1.0
CD2 A:HIS284 4.6 31.1 1.0
N A:LEU79 4.7 30.2 1.0
CA A:SER283 4.8 27.4 1.0
CB A:PRO82 4.9 41.8 1.0
CA A:LEU79 5.0 30.5 1.0
NE2 A:HIS201 5.0 48.2 1.0

Sodium binding site 2 out of 24 in 6vsu

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Sodium binding site 2 out of 24 in the Arginase From Arabidopsis Thaliana in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Arginase From Arabidopsis Thaliana in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:31.6
occ:1.00
 OG B:SER76 2.7 30.4 1.0
OE1 B:GLU313 2.8 27.1 1.0
O B:LEU79 2.8 26.6 1.0
O B:HOH645 2.9 26.1 1.0
OG B:SER283 2.9 27.8 1.0
CB B:SER76 3.3 31.1 1.0
CB B:SER283 3.4 28.7 1.0
CG B:PRO82 3.6 23.4 1.0
CD B:PRO82 3.8 23.8 1.0
CD B:GLU313 3.8 27.3 1.0
CE1 B:HIS201 3.8 31.9 1.0
O B:HOH527 3.9 21.9 1.0
ND1 B:HIS201 4.0 31.2 1.0
OE2 B:GLU313 4.0 29.0 1.0
C B:LEU79 4.0 27.1 1.0
CA B:SER76 4.4 32.0 1.0
CB B:ASP160 4.6 26.5 1.0
N B:LEU79 4.6 29.2 1.0
NE2 B:HIS284 4.6 29.5 1.0
CD2 B:HIS284 4.8 28.6 1.0
CA B:SER283 4.8 27.9 1.0
CB B:PRO82 4.8 22.9 1.0
CA B:LEU79 4.8 28.2 1.0
NE2 B:HIS201 4.9 32.9 1.0
N B:GLN80 5.0 27.4 1.0

Sodium binding site 3 out of 24 in 6vsu

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Sodium binding site 3 out of 24 in the Arginase From Arabidopsis Thaliana in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Arginase From Arabidopsis Thaliana in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:44.1
occ:1.00
 O C:HOH544 2.6 40.2 1.0
O C:LEU79 2.7 40.1 1.0
OG C:SER76 3.0 45.7 1.0
OG C:SER283 3.0 45.7 1.0
OE1 C:GLU313 3.0 39.5 1.0
CB C:SER76 3.2 46.4 1.0
CB C:SER283 3.4 45.9 1.0
CE1 C:HIS201 3.6 51.9 1.0
O C:HOH513 3.8 38.0 1.0
CD C:GLU313 3.8 40.6 1.0
ND1 C:HIS201 3.9 51.0 1.0
OE2 C:GLU313 3.9 43.0 1.0
C C:LEU79 3.9 40.3 1.0
CD C:PRO82 4.2 38.6 1.0
CA C:SER76 4.2 47.9 1.0
CG C:PRO82 4.2 37.8 1.0
NE2 C:HIS284 4.3 53.9 1.0
N C:LEU79 4.3 42.1 1.0
CA C:LEU79 4.6 41.1 1.0
CD2 C:HIS284 4.6 52.1 1.0
NE2 C:HIS201 4.6 53.4 1.0
CB C:ASP160 4.7 46.4 1.0
CA C:SER283 4.8 44.5 1.0
N C:SER77 4.9 48.0 1.0
CB C:LEU79 4.9 40.0 1.0
N C:GLN80 4.9 40.2 1.0
C C:SER76 5.0 48.7 1.0

Sodium binding site 4 out of 24 in 6vsu

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Sodium binding site 4 out of 24 in the Arginase From Arabidopsis Thaliana in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Arginase From Arabidopsis Thaliana in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na404

b:38.6
occ:1.00
 OE1 D:GLU313 2.7 27.8 1.0
O D:HOH633 2.8 20.6 1.0
OG D:SER283 2.8 24.3 1.0
OG D:SER76 2.8 28.1 1.0
O D:LEU79 2.9 28.1 1.0
CB D:SER283 3.2 24.7 1.0
CB D:SER76 3.4 29.6 1.0
CG D:PRO82 3.6 24.5 1.0
O D:HOH547 3.7 28.8 1.0
CD D:GLU313 3.7 26.8 1.0
CD D:PRO82 3.8 25.4 1.0
CE1 D:HIS201 3.8 33.5 1.0
OE2 D:GLU313 4.0 28.1 1.0
ND1 D:HIS201 4.0 32.2 1.0
C D:LEU79 4.2 28.9 1.0
CA D:SER76 4.5 30.1 1.0
NE2 D:HIS284 4.5 26.0 1.0
CD2 D:HIS284 4.5 24.3 1.0
CA D:SER283 4.6 24.4 1.0
CB D:ASP160 4.6 25.4 1.0
N D:LEU79 4.6 28.8 1.0
CB D:PRO82 4.8 24.8 1.0
CA D:LEU79 4.9 29.0 1.0
N D:SER283 4.9 23.3 1.0
NE2 D:HIS201 5.0 33.6 1.0

Sodium binding site 5 out of 24 in 6vsu

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Sodium binding site 5 out of 24 in the Arginase From Arabidopsis Thaliana in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Arginase From Arabidopsis Thaliana in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na403

b:32.5
occ:1.00
 OE1 E:GLU313 2.7 20.1 1.0
O E:LEU79 2.8 21.8 1.0
O E:HOH671 2.8 19.2 1.0
OG E:SER283 2.9 19.0 1.0
OG E:SER76 3.0 19.2 1.0
CB E:SER283 3.3 19.1 1.0
CB E:SER76 3.4 20.7 1.0
CG E:PRO82 3.6 17.6 1.0
CD E:GLU313 3.7 19.2 1.0
CD E:PRO82 3.8 18.6 1.0
O E:HOH514 3.8 20.9 1.0
CE1 E:HIS201 3.8 20.7 1.0
ND1 E:HIS201 4.0 19.6 1.0
OE2 E:GLU313 4.0 19.1 1.0
C E:LEU79 4.1 21.7 1.0
CA E:SER76 4.5 20.7 1.0
NE2 E:HIS284 4.5 21.7 1.0
CD2 E:HIS284 4.6 21.3 1.0
CB E:ASP160 4.6 19.7 1.0
N E:LEU79 4.7 21.9 1.0
CA E:SER283 4.7 18.9 1.0
CB E:PRO82 4.8 17.4 1.0
CA E:LEU79 4.9 22.4 1.0
NE2 E:HIS201 5.0 21.4 1.0
N E:SER283 5.0 17.4 1.0

Sodium binding site 6 out of 24 in 6vsu

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Sodium binding site 6 out of 24 in the Arginase From Arabidopsis Thaliana in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Arginase From Arabidopsis Thaliana in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na403

b:31.0
occ:1.00
 O F:HOH661 2.8 18.6 1.0
OE1 F:GLU313 2.8 26.1 1.0
OG F:SER283 2.8 21.9 1.0
OG F:SER76 2.9 29.9 1.0
O F:LEU79 3.0 26.0 1.0
CB F:SER283 3.3 21.2 1.0
CB F:SER76 3.4 29.7 1.0
CG F:PRO82 3.6 23.5 1.0
CD F:GLU313 3.7 26.2 1.0
CD F:PRO82 3.7 24.2 1.0
O F:HOH510 3.8 21.7 1.0
OE2 F:GLU313 3.9 28.0 1.0
CE1 F:HIS201 3.9 27.7 1.0
ND1 F:HIS201 4.0 26.6 1.0
C F:LEU79 4.2 26.7 1.0
CA F:SER76 4.5 29.7 1.0
CB F:ASP160 4.5 26.7 1.0
NE2 F:HIS284 4.6 23.7 1.0
CD2 F:HIS284 4.6 22.3 1.0
N F:LEU79 4.7 26.8 1.0
CA F:SER283 4.7 20.7 1.0
CB F:PRO82 4.8 24.4 1.0
CA F:LEU79 4.9 26.8 1.0
N F:SER283 5.0 19.7 1.0

Sodium binding site 7 out of 24 in 6vsu

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Sodium binding site 7 out of 24 in the Arginase From Arabidopsis Thaliana in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Arginase From Arabidopsis Thaliana in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na403

b:29.6
occ:1.00
 OG G:SER283 2.7 19.2 1.0
OE1 G:GLU313 2.7 19.7 1.0
O G:LEU79 2.8 20.6 1.0
O G:HOH598 2.9 20.6 1.0
OG G:SER76 3.0 20.6 1.0
CB G:SER283 3.3 18.7 1.0
CB G:SER76 3.4 21.8 1.0
CG G:PRO82 3.5 17.8 1.0
CD G:GLU313 3.7 19.7 1.0
CD G:PRO82 3.7 18.5 1.0
O G:HOH537 3.7 17.8 1.0
OE2 G:GLU313 3.9 21.2 1.0
CE1 G:HIS201 4.0 23.4 1.0
C G:LEU79 4.1 20.6 1.0
ND1 G:HIS201 4.1 21.8 1.0
CA G:SER76 4.5 22.2 1.0
NE2 G:HIS284 4.5 19.8 1.0
CB G:ASP160 4.5 20.0 1.0
CD2 G:HIS284 4.6 18.7 1.0
N G:LEU79 4.7 20.6 1.0
CA G:SER283 4.7 17.7 1.0
CB G:PRO82 4.7 17.5 1.0
CA G:LEU79 4.8 21.1 1.0
N G:SER283 5.0 16.4 1.0

Sodium binding site 8 out of 24 in 6vsu

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Sodium binding site 8 out of 24 in the Arginase From Arabidopsis Thaliana in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Arginase From Arabidopsis Thaliana in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na405

b:34.4
occ:1.00
 OE1 H:GLU313 2.7 24.4 1.0
O H:HOH635 2.8 31.5 1.0
OG H:SER283 2.9 26.1 1.0
O H:LEU79 3.0 28.1 1.0
OG H:SER76 3.0 29.0 1.0
CB H:SER283 3.3 26.1 1.0
CB H:SER76 3.3 29.4 1.0
CG H:PRO82 3.6 24.0 1.0
CD H:GLU313 3.7 23.8 1.0
O H:HOH519 3.7 28.8 1.0
CD H:PRO82 3.8 25.2 1.0
CE1 H:HIS201 3.8 30.9 1.0
ND1 H:HIS201 3.9 29.6 1.0
OE2 H:GLU313 3.9 24.4 1.0
C H:LEU79 4.2 28.8 1.0
CA H:SER76 4.5 29.5 1.0
NE2 H:HIS284 4.5 27.0 1.0
CD2 H:HIS284 4.5 25.8 1.0
CB H:ASP160 4.6 27.1 1.0
CA H:SER283 4.7 24.7 1.0
N H:LEU79 4.7 30.2 1.0
CB H:PRO82 4.7 23.9 1.0
CA H:LEU79 5.0 30.0 1.0

Sodium binding site 9 out of 24 in 6vsu

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Sodium binding site 9 out of 24 in the Arginase From Arabidopsis Thaliana in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Arginase From Arabidopsis Thaliana in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na403

b:33.6
occ:1.00
 OE1 I:GLU313 2.7 20.3 1.0
O I:HOH617 2.7 19.2 1.0
O I:LEU79 2.8 23.7 1.0
OG I:SER283 2.9 20.6 1.0
OG I:SER76 2.9 23.0 1.0
CB I:SER283 3.2 20.8 1.0
CB I:SER76 3.4 24.2 1.0
CD I:GLU313 3.6 21.5 1.0
CE1 I:HIS201 3.7 23.1 1.0
CG I:PRO82 3.8 21.8 1.0
O I:HOH516 3.8 19.3 1.0
OE2 I:GLU313 3.9 22.3 1.0
CD I:PRO82 3.9 22.1 1.0
ND1 I:HIS201 3.9 22.1 1.0
C I:LEU79 4.1 23.4 1.0
CA I:SER76 4.4 25.2 1.0
NE2 I:HIS284 4.4 20.7 1.0
CD2 I:HIS284 4.5 20.2 1.0
CB I:ASP160 4.5 22.8 1.0
N I:LEU79 4.7 23.2 1.0
CA I:SER283 4.7 20.6 1.0
NE2 I:HIS201 4.9 23.4 1.0
CA I:LEU79 4.9 23.4 1.0
N I:SER283 5.0 19.4 1.0
CB I:PRO82 5.0 22.2 1.0

Sodium binding site 10 out of 24 in 6vsu

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Sodium binding site 10 out of 24 in the Arginase From Arabidopsis Thaliana in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Arginase From Arabidopsis Thaliana in Complex with Ornithine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na403

b:29.8
occ:1.00
 O J:HOH680 2.7 16.9 1.0
OE1 J:GLU313 2.8 20.1 1.0
OG J:SER283 2.8 19.4 1.0
O J:LEU79 2.9 20.3 1.0
OG J:SER76 3.0 19.2 1.0
CB J:SER283 3.2 19.7 1.0
CB J:SER76 3.5 19.8 1.0
CG J:PRO82 3.6 17.4 1.0
O J:HOH559 3.7 21.1 1.0
CD J:GLU313 3.7 19.7 1.0
CE1 J:HIS201 3.8 19.8 1.0
CD J:PRO82 3.8 17.7 1.0
OE2 J:GLU313 4.0 20.2 1.0
ND1 J:HIS201 4.0 18.5 1.0
C J:LEU79 4.1 20.8 1.0
CD2 J:HIS284 4.5 19.0 1.0
CA J:SER76 4.5 19.4 1.0
NE2 J:HIS284 4.5 19.7 1.0
N J:LEU79 4.6 21.8 1.0
CA J:SER283 4.6 19.5 1.0
CB J:ASP160 4.7 19.1 1.0
CA J:LEU79 4.9 21.9 1.0
NE2 J:HIS201 4.9 19.8 1.0
CB J:PRO82 4.9 17.4 1.0
N J:SER283 4.9 18.4 1.0

Reference:

B.Sekula, B.Sekula. N/A N/A.
ISSN: ESSN 1664-462X
PubMed: 32754173
DOI: 10.3389/FPLS.2020.00987
Page generated: Tue Oct 8 14:26:10 2024

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