Sodium in PDB 4o0e: Crystal Structure of the Human L-Asparaginase Protein T186V Mutant

All present enzymatic activity of Crystal Structure of the Human L-Asparaginase Protein T186V Mutant:
3.4.19.5; 3.5.1.1;

The structure of Crystal Structure of the Human L-Asparaginase Protein T186V Mutant, PDB code: 4o0e 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)	28.45 / 1.71
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.378, 59.378, 298.322, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 22.5

The binding sites of Sodium atom in the Crystal Structure of the Human L-Asparaginase Protein T186V Mutant (pdb code 4o0e). 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 T186V Mutant, PDB code: 4o0e:
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 T186V 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 T186V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:33.4 occ:1.00 O A:ASP58 2.1 27.0 1.0 O A:CYS65 2.3 31.7 1.0 O A:PHE61 2.4 26.1 1.0 O A:LEU55 2.6 24.4 1.0 O A:ALA63 2.7 25.8 1.0 O A:GLU56 2.8 23.2 1.0 C A:ASP58 3.2 26.4 1.0 C A:PHE61 3.4 25.2 1.0 C A:GLU56 3.5 24.0 1.0 C A:CYS65 3.5 32.4 1.0 C A:LEU55 3.8 22.6 1.0 CA A:GLU56 3.8 23.4 1.0 C A:ALA63 3.9 26.1 1.0 N A:ASP58 4.0 23.7 1.0 N A:PHE61 4.0 28.9 1.0 CA A:PHE61 4.0 27.6 1.0 N A:PRO59 4.1 27.9 1.0 CB A:PHE61 4.1 29.1 1.0 N A:ALA63 4.1 23.6 1.0 CA A:ASP58 4.1 25.9 1.0 CA A:PRO59 4.1 28.9 1.0 CA A:GLY66 4.1 32.3 1.0 N A:GLU56 4.2 22.7 1.0 N A:GLY66 4.3 32.8 1.0 C A:ASP57 4.4 25.5 1.0 N A:ASP57 4.4 24.0 1.0 N A:CYS65 4.5 33.1 1.0 N A:ASN62 4.5 24.4 1.0 CA A:CYS65 4.5 34.9 1.0 C A:PRO59 4.5 28.1 1.0 C A:GLY66 4.6 30.5 1.0 CA A:ALA63 4.6 24.4 1.0 C A:GLY64 4.6 32.4 1.0 CB A:ASP58 4.7 26.0 1.0 N A:GLU60 4.8 27.0 1.0 N A:GLY64 4.9 26.4 1.0 N A:SER67 4.9 32.9 1.0 O A:ASP57 5.0 27.0 1.0 CA A:ASP57 5.0 25.2 1.0 O A:GLY64 5.0 32.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Human L-Asparaginase Protein T186V 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 T186V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:22.5 occ:1.00 O B:ALA63 2.1 18.3 1.0 O B:CYS65 2.3 26.3 1.0 O B:ASP58 2.4 27.6 1.0 O B:LEU55 2.6 24.7 1.0 O B:GLU56 2.8 29.5 1.0 O B:PHE61 2.8 25.9 1.0 C B:ALA63 3.3 22.9 1.0 C B:GLU56 3.3 27.0 1.0 C B:ASP58 3.4 28.7 1.0 C B:CYS65 3.4 29.0 1.0 CA B:GLU56 3.7 26.2 1.0 C B:PHE61 3.7 24.8 1.0 C B:LEU55 3.7 24.8 1.0 N B:CYS65 3.8 28.7 1.0 CB B:PHE61 3.9 28.9 1.0 N B:PHE61 3.9 28.3 1.0 N B:ASP58 3.9 27.6 1.0 N B:ALA63 3.9 22.3 1.0 CA B:PHE61 4.0 27.5 1.0 CA B:ALA63 4.1 20.9 1.0 CA B:CYS65 4.1 31.4 1.0 N B:GLU56 4.2 24.2 1.0 N B:PRO59 4.2 29.8 1.0 CA B:ASP58 4.2 29.4 1.0 C B:GLY64 4.2 27.6 1.0 N B:ASP57 4.3 28.3 1.0 CA B:PRO59 4.3 30.9 1.0 N B:GLY64 4.3 24.7 1.0 C B:PRO59 4.4 29.1 1.0 N B:GLY66 4.4 29.1 1.0 CB B:ALA63 4.4 20.9 1.0 C B:ASP57 4.5 29.0 1.0 CA B:GLY64 4.6 25.8 1.0 O B:PRO59 4.6 31.1 1.0 CB B:CYS65 4.6 34.4 1.0 CA B:GLY66 4.7 29.6 1.0 CB B:ASP58 4.7 30.8 1.0 N B:GLU60 4.8 28.6 1.0 O B:GLY64 4.8 29.4 1.0 CA B:ASP57 4.8 28.3 1.0 N B:ASN62 4.9 25.2 1.0 C B:GLU60 5.0 29.1 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