Sodium in PDB 1t3m: Structure of the Isoaspartyl Peptidase with L-Asparaginase Activity From E. Coli

All present enzymatic activity of Structure of the Isoaspartyl Peptidase with L-Asparaginase Activity From E. Coli:
3.5.1.1;

The structure of Structure of the Isoaspartyl Peptidase with L-Asparaginase Activity From E. Coli, PDB code: 1t3m was solved by A.Prahl, M.Pazgier, M.Hejazi, W.Lockau, J.Lubkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.318, 71.637, 149.583, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.7

The binding sites of Sodium atom in the Structure of the Isoaspartyl Peptidase with L-Asparaginase Activity From E. Coli (pdb code 1t3m). 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 the Isoaspartyl Peptidase with L-Asparaginase Activity From E. Coli, PDB code: 1t3m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Isoaspartyl Peptidase with L-Asparaginase Activity From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Isoaspartyl Peptidase with L-Asparaginase Activity From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:16.0 occ:1.00 O A:CYS62 2.3 16.2 1.0 O A:ILE69 2.3 13.3 1.0 O A:ALA67 2.3 14.5 1.0 O A:GLU60 2.5 14.5 1.0 O A:PHE65 2.6 12.9 1.0 O A:LEU59 2.8 14.1 1.0 C A:GLU60 3.1 14.6 1.0 C A:CYS62 3.3 13.7 1.0 C A:ILE69 3.5 14.9 1.0 CA A:GLU60 3.5 12.5 1.0 C A:ALA67 3.5 14.9 1.0 C A:PHE65 3.7 12.8 1.0 C A:LEU59 3.8 13.9 1.0 N A:CYS62 3.8 15.4 1.0 N A:ILE69 3.9 15.0 1.0 N A:ALA67 4.0 13.2 1.0 N A:PHE65 4.1 16.8 1.0 CA A:CYS62 4.1 18.6 1.0 N A:PRO63 4.2 16.0 0.5 N A:GLU60 4.2 13.6 1.0 C A:GLY68 4.2 15.9 1.0 N A:PRO63 4.2 15.4 0.5 CA A:PHE65 4.2 14.5 1.0 CA A:ILE69 4.2 14.2 1.0 CA A:PRO63 4.2 14.1 0.5 C A:GLU61 4.2 15.2 1.0 N A:GLU61 4.2 14.9 1.0 CB A:PHE65 4.2 13.3 1.0 CA A:ALA67 4.3 10.6 1.0 CA A:PRO63 4.3 14.5 0.5 CA A:GLY70 4.5 21.8 1.0 N A:GLY70 4.5 16.1 1.0 N A:GLY68 4.5 11.7 1.0 CA A:GLY68 4.6 13.0 1.0 C A:PRO63 4.6 14.4 0.5 O A:GLY68 4.6 13.1 1.0 C A:PRO63 4.6 14.3 0.5 CB A:ILE69 4.6 19.2 0.5 CB A:ALA67 4.7 15.7 1.0 O A:GLU61 4.7 16.1 1.0 CB A:CYS62 4.7 15.8 1.0 CA A:GLU61 4.7 13.4 1.0 N A:ASN66 4.8 13.5 1.0 CB A:ILE69 4.8 16.9 0.6 CB A:GLU60 4.8 13.1 1.0 O A:PRO63 5.0 17.1 0.5 C A:GLY70 5.0 20.2 1.0 O A:PRO63 5.0 17.3 0.5

Sodium binding site 2 out of 2 in the Structure of the Isoaspartyl Peptidase with L-Asparaginase Activity From E. Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Isoaspartyl Peptidase with L-Asparaginase Activity From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Na802 b:18.4 occ:1.00 O C:ILE69 2.2 18.8 1.0 O C:ALA67 2.2 16.4 1.0 O C:CYS62 2.4 16.8 1.0 O C:GLU60 2.4 16.8 1.0 O C:PHE65 2.6 15.2 1.0 O C:LEU59 2.9 17.5 1.0 C C:GLU60 3.2 19.0 1.0 C C:ILE69 3.3 16.9 1.0 C C:CYS62 3.4 18.9 1.0 C C:ALA67 3.5 14.4 1.0 CA C:GLU60 3.6 16.2 1.0 C C:PHE65 3.6 16.4 1.0 N C:ILE69 3.8 15.4 1.0 C C:LEU59 3.9 17.5 1.0 N C:CYS62 3.9 16.2 1.0 N C:ALA67 4.0 13.9 1.0 N C:PHE65 4.1 17.2 1.0 CA C:ILE69 4.1 18.2 1.0 C C:GLY68 4.1 14.6 1.0 N C:PRO63 4.1 19.9 1.0 CA C:PRO63 4.2 18.3 1.0 CA C:PHE65 4.2 17.8 1.0 CA C:CYS62 4.2 17.1 1.0 C C:GLU61 4.2 16.1 1.0 N C:GLU60 4.2 15.5 1.0 CA C:ALA67 4.3 12.7 1.0 N C:GLU61 4.3 17.4 1.0 CB C:PHE65 4.3 14.8 1.0 N C:GLY70 4.4 15.9 1.0 N C:GLY68 4.4 15.2 1.0 CA C:GLY68 4.5 17.0 1.0 C C:PRO63 4.5 16.6 1.0 CB C:ILE69 4.6 15.8 0.6 CA C:GLY70 4.6 16.7 1.0 O C:GLY68 4.6 14.3 1.0 O C:GLU61 4.7 18.9 1.0 CB C:ALA67 4.7 13.5 1.0 CB C:ILE69 4.7 17.0 0.5 CA C:GLU61 4.7 14.6 1.0 N C:ASN66 4.8 15.1 1.0 CB C:CYS62 4.8 16.2 1.0 CB C:GLU60 4.9 14.6 1.0 O C:PRO63 4.9 18.9 1.0 C C:GLY70 4.9 20.5 1.0 N C:LEU64 5.0 17.9 1.0 C C:ASN66 5.0 17.5 1.0

A.Prahl, M.Pazgier, M.Hejazi, W.Lockau, J.Lubkowski. Structure of the Isoaspartyl Peptidase with L-Asparaginase Activity From Escherichia Coli. Acta Crystallogr.,Sect.D V. 60 1173 2004.
ISSN: ISSN 0907-4449
PubMed: 15159592
DOI: 10.1107/S0907444904003403