Atomistry » Sodium » PDB 2fmp-2gg2 » 2gez
Atomistry »
  Sodium »
    PDB 2fmp-2gg2 »
      2gez »

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: Mon Oct 7 02:34:30 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy