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Sodium in PDB 2zak: Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation

Enzymatic activity of Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation

All present enzymatic activity of Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation:
3.4.19.5; 3.5.1.1;

Protein crystallography data

The structure of Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation, PDB code: 2zak was solved by K.Michalska, A.Hernandez-Santoyo, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.350, 77.780, 147.930, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25.3

Other elements in 2zak:

The structure of Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation (pdb code 2zak). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation, PDB code: 2zak:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2zak

Go back to Sodium Binding Sites List in 2zak
Sodium binding site 1 out of 2 in the Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na322

b:23.5
occ:1.00
O A:CYS63 2.3 23.0 1.0
O A:ALA68 2.3 23.9 1.0
O A:ILE70 2.3 22.4 1.0
O A:GLU61 2.4 21.4 1.0
O A:PHE66 2.5 23.1 1.0
O A:LEU60 2.7 22.5 1.0
C A:GLU61 3.2 22.6 1.0
C A:CYS63 3.3 23.5 1.0
C A:ILE70 3.5 23.6 1.0
C A:ALA68 3.5 23.7 1.0
CA A:GLU61 3.6 22.6 1.0
C A:PHE66 3.6 23.1 1.0
C A:LEU60 3.7 22.5 1.0
N A:CYS63 3.8 23.4 1.0
N A:ILE70 4.0 22.8 1.0
N A:PHE66 4.0 23.1 1.0
CA A:CYS63 4.0 24.2 1.0
N A:ALA68 4.1 23.5 1.0
N A:GLU61 4.1 22.4 1.0
CA A:PHE66 4.1 23.8 1.0
CA A:PRO64 4.2 23.0 1.0
N A:PRO64 4.2 23.2 1.0
N A:GLU62 4.2 23.4 1.0
CA A:ILE70 4.2 23.5 1.0
C A:GLU62 4.3 23.9 1.0
C A:GLY69 4.3 24.1 1.0
CB A:PHE66 4.3 23.4 1.0
CA A:ALA68 4.4 24.1 1.0
N A:GLY71 4.5 23.2 1.0
CB A:CYS63 4.5 24.3 1.0
N A:GLY69 4.5 23.6 1.0
C A:PRO64 4.5 22.8 1.0
CA A:GLY71 4.5 22.8 1.0
CB A:ILE70 4.7 24.2 1.0
CA A:GLY69 4.7 24.0 1.0
CB A:ALA68 4.7 23.9 1.0
N A:ASN67 4.7 22.3 1.0
O A:GLU62 4.8 23.1 1.0
O A:GLY69 4.8 24.0 1.0
CA A:GLU62 4.8 23.1 1.0
O A:PRO64 4.9 21.8 1.0
N A:LEU65 4.9 23.1 1.0
CB A:GLU61 4.9 22.2 1.0
C A:GLY71 5.0 22.8 1.0

Sodium binding site 2 out of 2 in 2zak

Go back to Sodium Binding Sites List in 2zak
Sodium binding site 2 out of 2 in the Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Orthorhombic Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na322

b:28.8
occ:1.00
O B:CYS63 2.3 24.0 1.0
O B:ILE70 2.3 21.2 1.0
O B:ALA68 2.5 22.6 1.0
O B:GLU61 2.5 24.3 1.0
O B:LEU60 2.6 20.6 1.0
O B:PHE66 2.8 23.3 1.0
C B:GLU61 3.2 23.8 1.0
C B:CYS63 3.3 23.7 1.0
C B:ILE70 3.5 23.3 1.0
CA B:GLU61 3.6 23.7 1.0
C B:ALA68 3.6 22.7 1.0
C B:LEU60 3.7 22.4 1.0
C B:PHE66 3.8 23.5 1.0
N B:ILE70 3.8 23.8 1.0
N B:CYS63 3.9 23.8 1.0
N B:PHE66 4.1 23.0 1.0
CA B:PRO64 4.1 23.4 1.0
N B:GLU61 4.1 22.3 1.0
CA B:CYS63 4.1 24.0 1.0
N B:PRO64 4.1 23.6 1.0
C B:GLU62 4.1 24.3 1.0
N B:GLU62 4.2 23.9 1.0
N B:ALA68 4.2 22.7 1.0
CA B:ILE70 4.2 23.5 1.0
C B:GLY69 4.2 23.7 1.0
CA B:PHE66 4.2 23.4 1.0
CB B:PHE66 4.2 23.8 1.0
C B:PRO64 4.4 23.5 1.0
O B:GLU62 4.4 24.9 1.0
CA B:ALA68 4.5 23.0 1.0
N B:GLY71 4.5 22.8 1.0
N B:GLY69 4.6 23.2 1.0
CA B:GLY69 4.6 23.0 1.0
CB B:CYS63 4.7 23.8 1.0
CA B:GLU62 4.7 23.9 1.0
CA B:GLY71 4.7 22.9 1.0
O B:GLY69 4.7 22.6 1.0
CB B:ILE70 4.7 24.1 1.0
CB B:ALA68 4.8 20.9 1.0
N B:LEU65 4.8 23.6 1.0
O B:PRO64 4.9 23.1 1.0
N B:ASN67 4.9 23.6 1.0
CB B:GLU61 4.9 23.1 1.0
C B:GLY71 5.0 23.4 1.0
CA B:LEU60 5.0 21.6 1.0

Reference:

K.Michalska, D.Borek, A.Hernandez-Santoyo, M.Jaskolski. Crystal Packing of Plant-Type L-Asparaginase From Escherichia Coli Acta Crystallogr.,Sect.D V. 64 309 2008.
ISSN: ISSN 0907-4449
PubMed: 18323626
DOI: 10.1107/S0907444907068072
Page generated: Tue Dec 15 06:00:59 2020

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