Sodium in PDB 4o0f: Crystal Structure of the Human L-Asparaginase Protein T219A Mutant

All present enzymatic activity of Crystal Structure of the Human L-Asparaginase Protein T219A Mutant:
3.4.19.5; 3.5.1.1;

The structure of Crystal Structure of the Human L-Asparaginase Protein T219A Mutant, PDB code: 4o0f 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)	29.59 / 1.92
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.471, 59.471, 299.241, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 21.5

The binding sites of Sodium atom in the Crystal Structure of the Human L-Asparaginase Protein T219A Mutant (pdb code 4o0f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Human L-Asparaginase Protein T219A Mutant, PDB code: 4o0f:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Human L-Asparaginase Protein T219A 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 T219A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:31.5 occ:1.00 O A:CYS65 2.1 24.5 1.0 O A:ASP58 2.3 29.6 1.0 O A:PHE61 2.5 24.9 1.0 O A:ALA63 2.5 23.1 1.0 O A:GLU56 2.8 19.9 1.0 O A:LEU55 2.9 25.2 1.0 C A:CYS65 3.2 27.5 1.0 C A:ASP58 3.4 29.4 1.0 C A:GLU56 3.5 21.6 1.0 N A:CYS65 3.5 26.8 1.0 C A:PHE61 3.6 25.1 1.0 C A:ALA63 3.7 22.1 1.0 CA A:GLU56 3.8 21.6 1.0 CA A:CYS65 3.9 26.9 1.0 C A:LEU55 4.0 23.3 1.0 C A:GLY64 4.0 23.9 1.0 N A:PHE61 4.0 25.4 1.0 CB A:PHE61 4.1 26.8 1.0 N A:ALA63 4.1 23.2 1.0 CA A:PHE61 4.1 25.6 1.0 CA A:PRO59 4.1 31.6 1.0 N A:ASP58 4.2 24.3 1.0 N A:GLY66 4.2 26.1 1.0 N A:PRO59 4.2 32.2 1.0 C A:PRO59 4.3 30.5 1.0 N A:GLU56 4.4 22.6 1.0 CA A:ASP58 4.4 26.8 1.0 CA A:GLY66 4.4 26.5 1.0 CB A:CYS65 4.4 29.7 1.0 O A:PRO59 4.4 32.0 1.0 CA A:GLY64 4.5 22.7 1.0 N A:ASP57 4.5 24.3 1.0 N A:GLY64 4.5 23.8 1.0 CA A:ALA63 4.5 23.8 1.0 C A:GLY66 4.6 24.9 1.0 O A:GLY64 4.6 24.8 1.0 C A:ASP57 4.7 24.5 1.0 O A:GLY66 4.7 23.0 1.0 N A:ASN62 4.7 24.0 1.0 N A:GLU60 4.8 28.4 1.0 CB A:ASP58 5.0 29.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Human L-Asparaginase Protein T219A 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 T219A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:20.4 occ:1.00 O A:LEU166 2.0 52.3 1.0 O A:HOH571 2.9 27.9 1.0 N A:GLY220 3.1 19.4 1.0 C A:LEU166 3.1 46.0 1.0 C A:GLY167 3.2 42.5 1.0 N A:THR168 3.4 36.0 1.0 O A:GLY220 3.5 19.7 1.0 OG1 A:THR168 3.5 27.9 1.0 CA A:GLY220 3.5 19.5 1.0 CA A:GLY167 3.5 41.9 1.0 N A:GLY11 3.6 26.7 1.0 O A:GLY167 3.6 45.8 1.0 CB A:THR168 3.6 30.1 1.0 N A:GLY167 3.7 48.9 1.0 C A:GLY220 3.9 19.2 1.0 CA A:GLY10 4.0 29.2 1.0 CA A:THR168 4.1 30.4 1.0 C A:ALA219 4.2 19.5 1.0 N A:LEU166 4.2 39.0 1.0 CA A:LEU166 4.3 42.8 1.0 C A:GLY10 4.3 29.6 1.0 N A:GLY403 4.4 31.1 1.0 O A:GLY11 4.4 29.9 1.0 CA A:ALA219 4.5 18.7 1.0 CA A:GLY11 4.5 29.6 1.0 CB A:ALA219 4.6 17.9 1.0 C A:GLY11 4.7 31.1 1.0 CA A:GLY403 4.9 32.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Human L-Asparaginase Protein T219A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Human L-Asparaginase Protein T219A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:29.6 occ:1.00 O B:CYS65 2.1 23.9 1.0 O B:ALA63 2.3 24.5 1.0 O B:GLU56 2.5 29.1 1.0 O B:ASP58 2.5 24.4 1.0 O B:LEU55 2.6 21.7 1.0 O B:PHE61 2.8 25.2 1.0 C B:ASP58 3.2 26.1 1.0 C B:CYS65 3.2 24.0 1.0 C B:GLU56 3.2 26.6 1.0 C B:ALA63 3.5 21.0 1.0 CA B:GLU56 3.6 24.6 1.0 C B:LEU55 3.7 22.6 1.0 C B:PHE61 3.8 26.7 1.0 N B:ASP58 3.8 24.3 1.0 N B:PRO59 3.9 27.6 1.0 N B:ALA63 4.0 22.0 1.0 N B:CYS65 4.0 23.4 1.0 N B:PHE61 4.0 29.6 1.0 CA B:ASP58 4.0 24.8 1.0 CA B:CYS65 4.1 24.1 1.0 N B:GLU56 4.1 22.6 1.0 N B:GLY66 4.2 22.7 1.0 CA B:PHE61 4.2 27.8 1.0 CA B:ALA63 4.2 21.6 1.0 CA B:PRO59 4.2 27.5 1.0 CA B:GLY66 4.2 22.1 1.0 C B:ASP57 4.2 26.4 1.0 C B:GLY64 4.3 23.1 1.0 CB B:PHE61 4.3 29.5 1.0 N B:ASP57 4.3 27.2 1.0 CB B:CYS65 4.5 25.4 1.0 CB B:ALA63 4.5 19.1 1.0 N B:GLY64 4.5 21.2 1.0 CA B:GLY64 4.7 21.0 1.0 CB B:ASP58 4.7 25.1 1.0 O B:ASP57 4.7 26.8 1.0 O B:GLY64 4.7 22.6 1.0 C B:PRO59 4.7 27.2 1.0 CA B:ASP57 4.8 26.8 1.0 C B:GLY66 4.9 21.8 1.0 N B:ASN62 4.9 27.6 1.0 N B:GLU60 4.9 26.4 1.0 CB B:GLU56 5.0 24.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Human L-Asparaginase Protein T219A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Human L-Asparaginase Protein T219A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:22.9 occ:1.00 OG1 B:THR168 3.3 25.6 1.0 N B:GLY220 3.3 28.4 1.0 N B:GLY11 3.4 32.4 1.0 C B:GLY167 3.5 32.9 1.0 CA B:GLY167 3.6 30.1 1.0 N B:THR168 3.6 30.9 1.0 CA B:GLY10 3.6 31.0 1.0 N B:GLY167 3.6 31.1 1.0 CA B:GLY220 3.7 27.4 1.0 CB B:THR168 3.8 27.4 1.0 CB B:ALA219 3.9 27.5 1.0 C B:GLY10 4.0 32.2 1.0 O B:GLY220 4.0 25.7 1.0 O B:GLY167 4.1 35.7 1.0 C B:ALA219 4.2 28.0 1.0 C B:GLY11 4.3 41.4 1.0 CA B:THR168 4.3 28.7 1.0 C B:GLY220 4.3 26.2 1.0 CA B:ALA219 4.3 27.6 1.0 CA B:GLY11 4.4 39.8 1.0 CA B:GLY404 4.4 25.8 1.0 O B:GLY11 4.4 44.8 1.0 CB B:ALA12 4.5 46.1 1.0 N B:GLY404 4.7 24.9 1.0 N B:ALA12 4.7 43.1 1.0 N B:GLY10 5.0 29.7 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