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Sodium in PDB 2gez: Crystal Structure of Potassium-Independent Plant Asparaginase

Enzymatic activity of Crystal Structure of Potassium-Independent Plant Asparaginase

All present enzymatic activity of Crystal Structure of Potassium-Independent Plant Asparaginase:
3.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Potassium-Independent Plant Asparaginase, PDB code: 2gez was solved by K.Michalska, G.Bujacz, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.680, 60.200, 114.630, 100.60, 92.90, 113.40
R / Rfree (%) 18.9 / 25.4

Other elements in 2gez:

The structure of Crystal Structure of Potassium-Independent Plant Asparaginase also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Potassium-Independent Plant Asparaginase (pdb code 2gez). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Potassium-Independent Plant Asparaginase, PDB code: 2gez:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2gez

Go back to Sodium Binding Sites List in 2gez
Sodium binding site 1 out of 4 in the Crystal Structure of Potassium-Independent Plant Asparaginase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Potassium-Independent Plant Asparaginase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:28.4
occ:1.00
O A:ALA67 2.3 26.8 1.0
O A:ILE69 2.4 26.1 1.0
O A:PHE65 2.4 24.1 1.0
O A:ILE62 2.5 24.8 1.0
O A:GLU60 2.6 23.2 1.0
C A:PHE65 3.4 24.5 1.0
C A:ILE62 3.5 25.2 1.0
C A:ALA67 3.5 25.6 1.0
C A:ILE69 3.5 26.8 1.0
C A:GLU60 3.5 23.7 1.0
O A:LEU59 3.6 24.3 1.0
N A:ALA67 3.9 24.4 1.0
N A:PHE65 3.9 24.9 1.0
CA A:GLU60 3.9 24.0 1.0
CA A:PHE65 4.0 24.9 1.0
CB A:PHE65 4.1 24.9 1.0
N A:ILE69 4.1 26.0 1.0
N A:GLU63 4.2 25.4 1.0
CA A:GLU63 4.2 25.7 1.0
CA A:ALA67 4.2 25.1 1.0
C A:GLY68 4.3 25.4 1.0
N A:ILE62 4.3 24.9 1.0
CA A:GLY70 4.3 27.1 1.0
N A:GLY70 4.4 27.0 1.0
C A:GLU63 4.4 25.3 1.0
CA A:ILE62 4.4 25.1 1.0
CA A:ILE69 4.5 26.8 1.0
N A:GLY68 4.5 25.3 1.0
CG2 A:ILE69 4.5 28.3 1.0
N A:ASN66 4.5 24.2 1.0
C A:GLY70 4.6 26.7 1.0
C A:LEU59 4.6 24.4 1.0
O A:GLY68 4.6 24.8 1.0
CB A:ALA67 4.6 24.6 1.0
CA A:GLY68 4.6 25.3 1.0
N A:ASN61 4.7 23.8 1.0
O A:GLU63 4.7 25.1 1.0
N A:GLU60 4.8 24.2 1.0
N A:HIS64 4.8 25.1 1.0
C A:ASN66 4.8 24.6 1.0
C A:ASN61 4.8 24.3 1.0
N A:SER71 4.9 26.4 1.0
O A:GLY70 5.0 26.5 1.0

Sodium binding site 2 out of 4 in 2gez

Go back to Sodium Binding Sites List in 2gez
Sodium binding site 2 out of 4 in the Crystal Structure of Potassium-Independent Plant Asparaginase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Potassium-Independent Plant Asparaginase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na400

b:16.7
occ:1.00
O C:ILE62 2.3 27.6 1.0
O C:ILE69 2.3 25.4 1.0
O C:ALA67 2.4 24.9 1.0
O C:PHE65 2.5 23.0 1.0
O C:GLU60 2.6 28.3 1.0
C C:GLU60 3.4 28.5 1.0
O C:LEU59 3.4 29.0 1.0
C C:ILE62 3.4 28.1 1.0
C C:ILE69 3.4 25.8 1.0
C C:PHE65 3.5 23.5 1.0
C C:ALA67 3.6 24.4 1.0
CA C:GLU60 3.9 28.6 1.0
N C:ALA67 3.9 24.4 1.0
N C:ILE62 4.0 28.2 1.0
N C:PHE65 4.1 24.4 1.0
CA C:PHE65 4.1 23.8 1.0
CB C:PHE65 4.1 24.1 1.0
CG2 C:ILE69 4.2 25.6 1.0
N C:ILE69 4.2 25.4 1.0
CA C:ILE62 4.2 28.1 1.0
N C:GLU63 4.3 28.6 1.0
CA C:ALA67 4.3 24.4 1.0
CA C:GLU63 4.3 29.2 1.0
N C:ASN61 4.3 28.3 1.0
N C:GLY70 4.3 26.3 1.0
C C:GLY68 4.3 25.0 1.0
CA C:ILE69 4.3 25.3 1.0
C C:LEU59 4.4 28.8 1.0
CA C:GLY70 4.4 26.0 1.0
C C:GLU63 4.5 27.5 1.0
C C:ASN61 4.5 28.3 1.0
N C:ASN66 4.6 23.3 1.0
N C:GLU60 4.6 28.9 1.0
N C:GLY68 4.6 24.3 1.0
CB C:ALA67 4.6 24.3 1.0
O C:GLY68 4.6 25.4 1.0
O C:GLU63 4.7 27.6 1.0
CB C:ILE62 4.7 28.2 1.0
C C:GLY70 4.7 26.2 1.0
CA C:ASN61 4.7 28.1 1.0
CA C:GLY68 4.8 24.4 1.0
N C:HIS64 4.9 25.9 1.0
CB C:ILE69 4.9 25.2 1.0
C C:ASN66 4.9 24.4 1.0

Sodium binding site 3 out of 4 in 2gez

Go back to Sodium Binding Sites List in 2gez
Sodium binding site 3 out of 4 in the Crystal Structure of Potassium-Independent Plant Asparaginase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Potassium-Independent Plant Asparaginase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na402

b:16.6
occ:1.00
O E:ILE69 2.4 24.9 1.0
O E:ILE62 2.4 28.7 1.0
O E:ALA67 2.4 25.2 1.0
O E:PHE65 2.5 25.3 1.0
O E:GLU60 2.5 25.6 1.0
C E:GLU60 3.3 26.1 1.0
O E:LEU59 3.4 25.6 1.0
C E:PHE65 3.5 24.9 1.0
C E:ILE62 3.5 29.2 1.0
C E:ILE69 3.5 25.2 1.0
C E:ALA67 3.6 24.2 1.0
CA E:GLU60 3.7 25.9 1.0
N E:ALA67 3.8 24.4 1.0
N E:ILE62 4.0 28.5 1.0
N E:PHE65 4.0 25.9 1.0
CB E:PHE65 4.0 25.7 1.0
CA E:PHE65 4.1 25.3 1.0
N E:ILE69 4.1 25.0 1.0
CA E:ALA67 4.2 24.4 1.0
CA E:ILE62 4.3 29.0 1.0
N E:ASN61 4.3 26.2 1.0
C E:GLY68 4.3 24.9 1.0
C E:LEU59 4.3 26.0 1.0
CA E:ILE69 4.3 24.9 1.0
CG2 E:ILE69 4.4 26.2 1.0
N E:GLY70 4.4 24.9 1.0
N E:GLU63 4.4 29.7 1.0
CA E:GLY70 4.5 24.5 1.0
N E:ASN66 4.5 24.1 1.0
C E:GLU63 4.5 28.5 1.0
C E:ASN61 4.5 27.9 1.0
N E:GLU60 4.5 26.1 1.0
CA E:GLU63 4.5 30.1 1.0
O E:GLU63 4.6 29.2 1.0
CB E:ALA67 4.6 24.2 1.0
N E:GLY68 4.6 24.3 1.0
O E:GLY68 4.6 25.4 1.0
CB E:ILE62 4.7 29.4 1.0
CA E:GLY68 4.7 24.3 1.0
CA E:ASN61 4.8 26.8 1.0
C E:ASN66 4.8 24.8 1.0
C E:GLY70 4.8 24.4 1.0
N E:HIS64 4.9 27.2 1.0
CB E:GLU60 4.9 26.0 1.0
CA E:ASN66 4.9 24.3 1.0
CB E:ILE69 5.0 25.1 1.0

Sodium binding site 4 out of 4 in 2gez

Go back to Sodium Binding Sites List in 2gez
Sodium binding site 4 out of 4 in the Crystal Structure of Potassium-Independent Plant Asparaginase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Potassium-Independent Plant Asparaginase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na403

b:36.1
occ:1.00
O G:ILE69 2.3 29.1 1.0
O G:ALA67 2.3 26.6 1.0
O G:PHE65 2.4 23.5 1.0
O G:ILE62 2.4 24.9 1.0
O G:GLU60 2.6 25.6 1.0
C G:ILE69 3.4 28.5 1.0
C G:PHE65 3.4 23.9 1.0
C G:ILE62 3.4 25.3 1.0
C G:ALA67 3.5 26.4 1.0
C G:GLU60 3.6 25.5 1.0
O G:LEU59 3.8 26.2 1.0
N G:PHE65 3.9 23.4 1.0
N G:ALA67 3.9 25.9 1.0
CA G:PHE65 4.0 23.7 1.0
CA G:GLY70 4.0 27.9 1.0
CA G:GLU60 4.0 25.6 1.0
CA G:GLU63 4.0 24.8 1.0
N G:ILE69 4.1 27.7 1.0
N G:GLY70 4.1 28.3 1.0
CB G:PHE65 4.1 23.7 1.0
N G:GLU63 4.2 25.2 1.0
C G:GLU63 4.2 24.2 1.0
CA G:ALA67 4.3 26.1 1.0
N G:ILE62 4.3 25.6 1.0
C G:GLY68 4.3 26.8 1.0
CA G:ILE69 4.3 28.4 1.0
C G:GLY70 4.4 28.0 1.0
CA G:ILE62 4.5 25.3 1.0
O G:GLU63 4.5 23.9 1.0
N G:GLY68 4.5 26.2 1.0
N G:ASN66 4.6 24.3 1.0
CG2 G:ILE69 4.6 29.9 1.0
N G:HIS64 4.6 23.6 1.0
CB G:ALA67 4.7 25.9 1.0
N G:ASN61 4.7 25.4 1.0
C G:LEU59 4.7 26.2 1.0
CA G:GLY68 4.7 26.4 1.0
N G:SER71 4.7 27.7 1.0
C G:ASN61 4.8 25.4 1.0
O G:GLY68 4.8 26.1 1.0
N G:GLU60 4.9 25.8 1.0
C G:ASN66 4.9 25.2 1.0
O G:GLY70 5.0 28.4 1.0
CA G:ASN66 5.0 24.9 1.0

Reference:

K.Michalska, G.Bujacz, M.Jaskolski. Crystal Structure of Plant Asparaginase. J.Mol.Biol. V. 360 105 2006.
ISSN: ISSN 0022-2836
PubMed: 16725155
DOI: 10.1016/J.JMB.2006.04.066
Page generated: Tue Dec 15 05:49:34 2020

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