Sodium in PDB 4osx: Structure of Uncleaved Glycine-Bound Human L-Asparaginase Protein

All present enzymatic activity of Structure of Uncleaved Glycine-Bound Human L-Asparaginase Protein:
3.4.19.5; 3.5.1.1;

The structure of Structure of Uncleaved Glycine-Bound Human L-Asparaginase Protein, PDB code: 4osx 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)	29.39 / 1.95
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.940, 59.940, 301.100, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.9

The binding sites of Sodium atom in the Structure of Uncleaved Glycine-Bound Human L-Asparaginase Protein (pdb code 4osx). 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 Uncleaved Glycine-Bound Human L-Asparaginase Protein, PDB code: 4osx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Uncleaved Glycine-Bound Human L-Asparaginase Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Uncleaved Glycine-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:22.9 occ:1.00 O A:CYS65 2.2 24.8 1.0 O A:ASP58 2.3 20.5 1.0 O A:ALA63 2.4 20.3 1.0 O A:GLU56 2.6 20.9 1.0 O A:PHE61 2.6 21.3 1.0 O A:LEU55 3.0 20.1 1.0 C A:ASP58 3.2 21.0 1.0 C A:GLU56 3.4 20.6 1.0 C A:CYS65 3.4 24.7 1.0 C A:ALA63 3.6 20.5 1.0 C A:PHE61 3.6 21.3 1.0 CA A:GLU56 3.9 20.9 1.0 N A:PHE61 3.9 21.8 1.0 N A:ASP58 3.9 20.3 1.0 N A:CYS65 4.0 23.6 1.0 CA A:PHE61 4.0 21.2 1.0 N A:ALA63 4.0 20.0 1.0 N A:PRO59 4.0 21.5 1.0 C A:LEU55 4.1 20.5 1.0 CA A:PRO59 4.1 22.1 1.0 CA A:ASP58 4.1 20.4 1.0 CB A:PHE61 4.1 21.1 1.0 CA A:CYS65 4.2 24.7 1.0 C A:ASP57 4.2 20.4 1.0 N A:ASP57 4.3 20.6 1.0 C A:PRO59 4.3 22.1 1.0 N A:GLY66 4.3 25.0 1.0 CA A:ALA63 4.4 20.2 1.0 C A:GLY64 4.4 22.7 1.0 CA A:GLY66 4.5 25.1 1.0 N A:GLU56 4.5 20.3 1.0 O A:PRO59 4.5 21.8 1.0 O A:ASP57 4.5 20.7 1.0 N A:GLY64 4.6 20.7 1.0 CB A:CYS65 4.6 25.3 1.0 CA A:ASP57 4.7 20.5 1.0 CB A:ASP58 4.7 20.3 1.0 N A:GLU60 4.7 22.1 1.0 CA A:GLY64 4.8 21.8 1.0 N A:ASN62 4.8 21.1 1.0 C A:GLY66 4.9 25.0 1.0 O A:GLY64 4.9 22.1 1.0 CB A:ALA63 4.9 20.0 1.0

Sodium binding site 2 out of 2 in the Structure of Uncleaved Glycine-Bound Human L-Asparaginase Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Uncleaved Glycine-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:19.0 occ:1.00 O B:ASP58 2.2 26.4 1.0 O B:ALA63 2.4 22.8 1.0 O B:CYS65 2.4 24.9 1.0 O B:LEU55 2.4 23.3 1.0 O B:GLU56 2.8 24.9 1.0 O B:PHE61 2.9 24.1 1.0 C B:ASP58 3.2 26.3 1.0 C B:GLU56 3.4 24.9 1.0 C B:CYS65 3.5 24.5 1.0 C B:LEU55 3.5 23.2 1.0 C B:ALA63 3.5 22.3 1.0 CA B:GLU56 3.6 24.2 1.0 C B:PHE61 3.7 24.3 1.0 N B:ASP58 3.8 25.7 1.0 N B:GLU56 4.0 23.2 1.0 N B:ALA63 4.0 21.9 1.0 CA B:ASP58 4.0 25.9 1.0 N B:CYS65 4.1 24.2 1.0 CB B:PHE61 4.1 25.1 1.0 C B:GLY64 4.1 23.8 1.0 N B:PHE61 4.2 25.3 1.0 CA B:PHE61 4.2 25.1 1.0 N B:PRO59 4.2 26.2 1.0 CA B:CYS65 4.3 24.5 1.0 CA B:PRO59 4.3 26.6 1.0 N B:GLY66 4.3 24.5 1.0 CA B:ALA63 4.3 22.3 1.0 O B:GLY64 4.4 23.0 1.0 N B:ASP57 4.4 25.4 1.0 CA B:GLY66 4.4 24.7 1.0 C B:ASP57 4.5 25.7 1.0 N B:GLY64 4.5 22.7 1.0 CB B:ASP58 4.6 26.2 1.0 CA B:GLY64 4.6 22.9 1.0 CB B:ALA63 4.7 21.8 1.0 N B:ASN62 4.7 23.6 1.0 C B:PRO59 4.7 26.6 1.0 CB B:CYS65 4.8 24.7 1.0 CA B:LEU55 4.8 23.1 1.0 C B:GLY66 4.9 24.6 1.0 N B:GLU60 4.9 26.6 1.0 CB B:GLU56 5.0 24.1 1.0 CA B:ASP57 5.0 25.6 1.0 C B:ASN62 5.0 22.6 1.0

Y.Su, C.S.Karamitros, J.Nomme, T.Mcsorley, M.Konrad, A.Lavie. Free Glycine Accelerates the Autoproteolytic Activation of Human Asparaginase. Chem.Biol. V. 20 533 2013.
ISSN: ISSN 1074-5521
PubMed: 23601642
DOI: 10.1016/J.CHEMBIOL.2013.03.006