Sodium in PDB 1jn9: Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene

All present enzymatic activity of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene:
3.5.1.1;

The structure of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene, PDB code: 1jn9 was solved by D.Borek, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.941, 70.425, 148.862, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 23.2

The structure of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Calcium	(Ca)	3 atoms

The binding sites of Sodium atom in the Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene (pdb code 1jn9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene, PDB code: 1jn9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:16.0 occ:1.00 O A:ILE70 2.2 13.4 1.0 O A:CME63 2.2 15.5 1.0 O A:ALA68 2.2 13.8 1.0 O A:GLU61 2.5 15.2 1.0 O A:PHE66 2.7 12.2 1.0 O A:LEU60 2.7 15.7 1.0 C A:CME63 3.2 13.8 1.0 C A:GLU61 3.2 15.7 1.0 C A:ILE70 3.4 12.7 1.0 C A:ALA68 3.5 12.9 1.0 CA A:GLU61 3.6 15.9 1.0 C A:PHE66 3.7 12.6 1.0 N A:CME63 3.7 14.4 1.0 N A:ILE70 3.8 12.3 1.0 C A:LEU60 3.8 16.3 1.0 CA A:CME63 4.0 15.4 1.0 N A:ALA68 4.0 12.8 1.0 N A:PHE66 4.1 13.9 1.0 N A:PRO64 4.1 15.6 1.0 CA A:ILE70 4.1 12.1 1.0 CA A:PRO64 4.1 15.4 1.0 C A:GLY69 4.2 12.1 1.0 N A:GLU61 4.2 16.1 1.0 CA A:PHE66 4.2 13.2 1.0 C A:GLU62 4.2 15.3 1.0 CB A:PHE66 4.2 13.9 1.0 N A:GLU62 4.2 14.9 1.0 CA A:ALA68 4.3 13.1 1.0 N A:GLY71 4.4 12.5 1.0 N A:GLY69 4.5 12.9 1.0 C A:PRO64 4.5 15.3 1.0 CB A:ILE70 4.5 12.1 1.0 CA A:GLY69 4.5 12.9 1.0 O A:GLU62 4.6 15.1 1.0 CA A:GLY71 4.6 12.1 1.0 O A:GLY69 4.7 12.1 1.0 CB A:ALA68 4.7 13.7 1.0 CA A:GLU62 4.7 15.4 1.0 CB A:CME63 4.8 15.3 1.0 O A:PRO64 4.8 14.0 1.0 N A:ASN67 4.8 11.8 1.0 CB A:GLU61 4.9 16.3 1.0 N A:LEU65 4.9 14.9 1.0

Sodium binding site 2 out of 2 in the Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:18.5 occ:1.00 O C:ILE70 2.2 13.2 1.0 O C:CME63 2.3 15.0 1.0 O C:GLU61 2.4 11.9 1.0 O C:ALA68 2.5 16.2 1.0 O C:PHE66 2.6 14.4 1.0 O C:LEU60 2.6 13.9 1.0 C C:CME63 3.1 14.0 1.0 C C:GLU61 3.2 13.1 1.0 C C:ILE70 3.4 12.8 1.0 C C:PHE66 3.6 14.4 1.0 CA C:GLU61 3.6 13.1 1.0 C C:ALA68 3.7 15.2 1.0 C C:LEU60 3.7 13.6 1.0 N C:CME63 3.8 14.2 1.0 N C:ILE70 3.9 13.4 1.0 CA C:CME63 3.9 14.6 1.0 N C:PRO64 4.0 14.9 1.0 N C:PHE66 4.0 14.2 1.0 N C:ALA68 4.1 14.3 1.0 CA C:PRO64 4.1 15.1 1.0 C C:GLU62 4.1 13.7 1.0 CA C:PHE66 4.1 14.2 1.0 N C:GLU62 4.2 13.6 1.0 CA C:ILE70 4.2 13.0 1.0 N C:GLU61 4.2 13.2 1.0 CB C:PHE66 4.3 14.5 1.0 C C:GLY69 4.3 13.9 1.0 CA C:ALA68 4.4 14.7 1.0 C C:PRO64 4.4 14.4 1.0 N C:GLY71 4.5 12.5 1.0 CB C:ILE70 4.5 13.2 1.0 CB C:CME63 4.6 15.1 1.0 O C:GLU62 4.6 13.8 1.0 CA C:GLU62 4.7 13.8 1.0 CA C:GLY71 4.7 11.8 1.0 CB C:ALA68 4.7 15.2 1.0 N C:GLY69 4.7 15.3 1.0 N C:ASN67 4.7 14.1 1.0 CA C:GLY69 4.8 14.7 1.0 O C:GLY69 4.8 12.1 1.0 O C:PRO64 4.8 14.5 1.0 N C:LEU65 4.9 14.4 1.0 CB C:GLU61 5.0 13.0 1.0

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