Sodium in PDB 4o0g: Crystal Structure of the Human L-Asparaginase Protein T219V Mutant

All present enzymatic activity of Crystal Structure of the Human L-Asparaginase Protein T219V Mutant:
3.4.19.5; 3.5.1.1;

The structure of Crystal Structure of the Human L-Asparaginase Protein T219V Mutant, PDB code: 4o0g 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)	29.18 / 2.10
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.439, 59.439, 306.794, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 23.6

The binding sites of Sodium atom in the Crystal Structure of the Human L-Asparaginase Protein T219V Mutant (pdb code 4o0g). 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 T219V Mutant, PDB code: 4o0g:
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 T219V 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 T219V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:31.1 occ:1.00 O A:CYS65 2.1 33.5 1.0 O A:ALA63 2.3 27.7 1.0 O A:GLU56 2.4 28.8 1.0 O A:ASP58 2.6 41.6 1.0 O A:PHE61 2.7 30.8 1.0 O A:LEU55 2.9 23.4 1.0 C A:CYS65 3.2 28.1 1.0 C A:GLU56 3.2 28.0 1.0 C A:ASP58 3.5 37.9 1.0 C A:ALA63 3.5 25.4 1.0 CA A:GLU56 3.6 21.9 1.0 N A:CYS65 3.6 29.5 1.0 C A:PHE61 3.7 28.9 1.0 CA A:CYS65 3.9 31.4 1.0 C A:GLY64 3.9 29.6 1.0 C A:LEU55 4.0 20.8 1.0 CA A:PRO59 4.0 37.1 1.0 N A:ALA63 4.0 25.6 1.0 N A:ASP58 4.1 32.6 1.0 N A:PRO59 4.1 37.9 1.0 N A:GLY66 4.2 29.6 1.0 N A:PHE61 4.2 30.9 1.0 CA A:PHE61 4.2 30.4 1.0 N A:ASP57 4.3 29.2 1.0 N A:GLU56 4.3 18.6 1.0 CB A:PHE61 4.3 29.6 1.0 O A:GLY64 4.3 37.3 1.0 C A:PRO59 4.3 38.0 1.0 CA A:ALA63 4.4 24.3 1.0 N A:GLY64 4.4 28.7 1.0 CA A:GLY66 4.4 29.2 1.0 CB A:CYS65 4.4 30.9 1.0 C A:ASP57 4.4 30.6 1.0 CA A:ASP58 4.4 33.9 1.0 CA A:GLY64 4.4 29.2 1.0 O A:PRO59 4.6 36.0 1.0 C A:GLY66 4.6 28.8 1.0 N A:ASN62 4.7 26.8 1.0 CA A:ASP57 4.8 31.0 1.0 CB A:GLU56 4.8 22.2 1.0 N A:SER67 4.9 28.0 1.0 O A:ASP57 4.9 31.5 1.0 N A:GLU60 4.9 34.9 1.0 CB A:ALA63 4.9 23.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Human L-Asparaginase Protein T219V 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 T219V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:24.8 occ:1.00 O B:CYS65 2.4 32.0 1.0 O B:ASP58 2.4 30.3 1.0 O B:ALA63 2.4 25.5 1.0 O B:LEU55 2.5 22.4 1.0 O B:GLU56 2.7 25.2 1.0 O B:PHE61 2.9 33.0 1.0 C B:GLU56 3.1 25.6 1.0 C B:ASP58 3.3 27.6 1.0 C B:CYS65 3.5 26.9 1.0 CA B:GLU56 3.5 23.0 1.0 N B:ASP58 3.5 26.7 1.0 C B:LEU55 3.6 23.0 1.0 C B:ALA63 3.6 24.3 1.0 C B:PHE61 3.7 29.2 1.0 CB B:PHE61 3.8 28.6 1.0 N B:CYS65 3.8 26.0 1.0 N B:ASP57 3.9 25.1 1.0 CA B:ASP58 3.9 26.3 1.0 N B:PHE61 4.0 30.4 1.0 CA B:PHE61 4.0 29.6 1.0 N B:GLU56 4.0 21.3 1.0 C B:ASP57 4.1 25.8 1.0 N B:PRO59 4.2 25.7 1.0 CA B:CYS65 4.2 28.0 1.0 C B:GLY64 4.4 26.8 1.0 N B:ALA63 4.4 24.3 1.0 CB B:ALA63 4.4 23.6 1.0 CA B:ALA63 4.5 24.0 1.0 N B:GLY66 4.5 26.8 1.0 CA B:PRO59 4.5 26.2 1.0 CA B:ASP57 4.5 25.2 1.0 CB B:ASP58 4.6 28.3 1.0 N B:GLY64 4.6 26.1 1.0 CB B:CYS65 4.7 26.6 1.0 CA B:GLY66 4.7 24.9 1.0 CA B:GLY64 4.7 26.6 1.0 O B:ASP57 4.8 24.4 1.0 C B:PRO59 4.8 28.3 1.0 CA B:LEU55 4.8 24.6 1.0 CB B:GLU56 4.9 22.4 1.0 N B:ASN62 4.9 25.1 1.0 CG B:PHE61 5.0 29.3 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