Sodium in PDB 4o0d: Crystal Structure of the Human L-Asparaginase Protein T168S Mutant

All present enzymatic activity of Crystal Structure of the Human L-Asparaginase Protein T168S Mutant:
3.4.19.5; 3.5.1.1;

The structure of Crystal Structure of the Human L-Asparaginase Protein T168S Mutant, PDB code: 4o0d was solved by J.Nomme, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.27 / 1.95
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.700, 59.700, 299.700, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 23.4

The binding sites of Sodium atom in the Crystal Structure of the Human L-Asparaginase Protein T168S Mutant (pdb code 4o0d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Human L-Asparaginase Protein T168S Mutant, PDB code: 4o0d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Human L-Asparaginase Protein T168S Mutant


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 the Human L-Asparaginase Protein T168S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:14.8 occ:1.00 O A:CYS65 2.2 20.0 1.0 O A:ASP58 2.3 22.0 1.0 O A:ALA63 2.5 18.3 1.0 O A:GLU56 2.7 19.3 1.0 O A:PHE61 2.8 18.9 1.0 O A:LEU55 2.8 16.5 1.0 C A:ASP58 3.3 21.9 1.0 C A:CYS65 3.3 18.6 1.0 C A:GLU56 3.3 19.6 1.0 C A:ALA63 3.7 16.6 1.0 CA A:GLU56 3.7 18.5 1.0 C A:PHE61 3.7 19.1 1.0 C A:LEU55 3.8 16.1 1.0 N A:CYS65 3.9 19.1 1.0 N A:PHE61 4.0 19.4 1.0 N A:ASP58 4.0 21.4 1.0 CA A:CYS65 4.0 19.5 1.0 N A:ALA63 4.1 16.6 1.0 N A:PRO59 4.1 23.4 1.0 CA A:PRO59 4.2 21.8 1.0 CA A:PHE61 4.2 18.9 1.0 C A:GLY64 4.2 18.3 1.0 CA A:ASP58 4.2 22.4 1.0 C A:ASP57 4.3 23.8 1.0 N A:GLU56 4.3 16.5 1.0 CB A:PHE61 4.3 19.5 1.0 N A:GLY66 4.3 18.2 1.0 CB A:CYS65 4.3 19.7 1.0 N A:ASP57 4.3 21.2 1.0 C A:PRO59 4.4 20.8 1.0 CA A:ALA63 4.5 16.6 1.0 O A:GLY64 4.5 18.0 1.0 CA A:GLY66 4.5 19.4 1.0 O A:ASP57 4.6 27.6 1.0 N A:GLU60 4.7 19.1 1.0 N A:GLY64 4.7 17.6 1.0 CA A:GLY64 4.8 17.8 1.0 CA A:ASP57 4.8 23.2 1.0 CB A:ASP58 4.8 22.3 1.0 O A:PRO59 4.8 19.6 1.0 N A:ASN62 4.9 17.9 1.0 C A:GLY66 4.9 18.9 1.0 CB A:ALA63 4.9 16.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Human L-Asparaginase Protein T168S Mutant


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 the Human L-Asparaginase Protein T168S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:14.0 occ:1.00 O B:ALA63 2.0 12.0 1.0 O B:ASP58 2.3 19.2 1.0 O B:CYS65 2.4 15.3 1.0 O B:LEU55 2.5 17.0 1.0 O B:PHE61 2.6 17.4 1.0 O B:GLU56 3.0 18.5 1.0 C B:ALA63 3.2 11.9 1.0 C B:ASP58 3.4 19.6 1.0 C B:CYS65 3.5 15.4 1.0 C B:PHE61 3.5 16.3 1.0 C B:GLU56 3.6 18.6 1.0 N B:ALA63 3.6 11.7 1.0 C B:LEU55 3.7 18.8 1.0 CA B:GLU56 3.7 17.7 1.0 N B:CYS65 3.9 15.9 1.0 CA B:ALA63 3.9 11.8 1.0 CB B:PHE61 4.0 16.8 1.0 N B:PHE61 4.0 17.4 1.0 CA B:PHE61 4.0 16.5 1.0 N B:ASP58 4.1 18.8 1.0 N B:GLU56 4.2 17.3 1.0 N B:GLY64 4.2 13.1 1.0 C B:GLY64 4.2 14.4 1.0 N B:PRO59 4.3 19.9 1.0 CA B:ASP58 4.3 20.0 1.0 CA B:PRO59 4.3 19.4 1.0 CA B:CYS65 4.3 16.2 1.0 N B:GLY66 4.4 15.0 1.0 CA B:GLY66 4.4 15.2 1.0 CA B:GLY64 4.4 13.7 1.0 CB B:ALA63 4.5 11.2 1.0 N B:ASN62 4.6 14.2 1.0 N B:ASP57 4.6 19.6 1.0 C B:GLY66 4.6 15.5 1.0 C B:ASN62 4.7 12.5 1.0 C B:PRO59 4.7 19.7 1.0 C B:ASP57 4.8 19.4 1.0 O B:GLY64 4.9 13.8 1.0 N B:SER67 4.9 15.7 1.0 CB B:ASP58 4.9 20.5 1.0 CA B:LEU55 4.9 19.9 1.0 O B:GLY66 5.0 15.4 1.0 CA B:ASN62 5.0 13.4 1.0

J.Nomme, Y.Su, A.Lavie. Elucidation of the Specific Function of the Conserved Threonine Triad Responsible For Human L-Asparaginase Autocleavage and Substrate Hydrolysis. J.Mol.Biol. V. 426 2471 2014.
ISSN: ISSN 0022-2836
PubMed: 24768817
DOI: 10.1016/J.JMB.2014.04.016