Sodium in PDB 4osy: Structure of Fully-Cleaved Glycine-Bound Human L-Asparaginase Protein

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

The structure of Structure of Fully-Cleaved Glycine-Bound Human L-Asparaginase Protein, PDB code: 4osy 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)	29.72 / 1.91
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.736, 59.736, 301.527, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.4

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

Sodium binding site 1 out of 2 in the Structure of Fully-Cleaved 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 Fully-Cleaved Glycine-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:30.4 occ:1.00 O A:CYS65 2.2 30.8 1.0 O A:ALA63 2.2 29.1 1.0 O A:LEU55 2.6 29.4 1.0 O A:ASP58 2.6 32.5 1.0 O A:GLU56 2.8 30.7 1.0 O A:PHE61 2.9 28.0 1.0 C A:GLU56 3.3 30.8 1.0 C A:ASP58 3.4 32.6 1.0 C A:CYS65 3.4 30.8 1.0 C A:ALA63 3.5 28.4 1.0 CA A:GLU56 3.6 30.1 1.0 C A:LEU55 3.7 29.5 1.0 N A:CYS65 3.8 30.6 1.0 C A:PHE61 3.8 28.4 1.0 N A:ASP58 3.8 32.1 1.0 N A:PRO59 4.1 32.8 1.0 CA A:CYS65 4.1 31.3 1.0 N A:GLU56 4.1 29.6 1.0 C A:GLY64 4.1 30.2 1.0 N A:ALA63 4.1 27.7 1.0 N A:PHE61 4.2 30.1 1.0 CA A:ASP58 4.2 32.1 1.0 CB A:PHE61 4.2 28.9 1.0 CA A:PRO59 4.2 32.8 1.0 N A:ASP57 4.2 31.1 1.0 CA A:PHE61 4.2 29.1 1.0 N A:GLY66 4.4 30.9 1.0 N A:GLY64 4.4 28.8 1.0 CA A:ALA63 4.4 28.1 1.0 CA A:GLY64 4.4 29.4 1.0 C A:ASP57 4.4 32.0 1.0 CB A:CYS65 4.5 31.4 1.0 CA A:GLY66 4.5 31.4 1.0 C A:PRO59 4.7 32.4 1.0 O A:GLY64 4.7 30.0 1.0 CA A:ASP57 4.8 32.0 1.0 CB A:ALA63 4.8 27.3 1.0 C A:GLY66 4.9 31.5 1.0 N A:ASN62 5.0 28.0 1.0 CB A:GLU56 5.0 29.8 1.0 CA A:LEU55 5.0 29.6 1.0 N A:GLU60 5.0 32.2 1.0 CB A:ASP58 5.0 32.4 1.0

Sodium binding site 2 out of 2 in the Structure of Fully-Cleaved 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 Fully-Cleaved Glycine-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:35.8 occ:1.00 O B:ASP58 2.3 30.0 1.0 O B:CYS65 2.3 32.1 1.0 O B:ALA63 2.3 28.6 1.0 O B:PHE61 2.6 28.1 1.0 O B:GLU56 2.7 28.6 1.0 O B:LEU55 2.8 28.9 1.0 C B:ASP58 3.3 30.2 1.0 C B:CYS65 3.4 32.0 1.0 C B:GLU56 3.4 29.0 1.0 C B:ALA63 3.5 28.1 1.0 C B:PHE61 3.6 28.3 1.0 CA B:GLU56 3.8 28.4 1.0 C B:LEU55 3.9 28.8 1.0 N B:ALA63 3.9 26.9 1.0 N B:CYS65 4.0 31.4 1.0 N B:PHE61 4.0 29.8 1.0 N B:ASP58 4.0 29.9 1.0 CA B:PHE61 4.1 29.2 1.0 CB B:PHE61 4.1 29.5 1.0 CA B:ASP58 4.2 29.8 1.0 C B:GLY64 4.2 30.7 1.0 CA B:CYS65 4.2 32.3 1.0 N B:PRO59 4.3 30.6 1.0 N B:GLY66 4.3 32.3 1.0 N B:GLU56 4.3 28.5 1.0 CA B:ALA63 4.3 27.7 1.0 CA B:PRO59 4.3 30.9 1.0 CA B:GLY66 4.3 32.5 1.0 C B:ASP57 4.4 29.8 1.0 N B:ASP57 4.4 29.3 1.0 N B:GLY64 4.5 28.7 1.0 C B:PRO59 4.5 30.5 1.0 CA B:GLY64 4.6 29.6 1.0 O B:GLY64 4.6 30.2 1.0 CB B:ASP58 4.7 30.0 1.0 C B:GLY66 4.7 32.8 1.0 N B:ASN62 4.7 27.8 1.0 O B:ASP57 4.7 30.4 1.0 O B:PRO59 4.8 30.6 1.0 CB B:CYS65 4.8 32.2 1.0 CB B:ALA63 4.8 26.9 1.0 N B:GLU60 4.9 30.8 1.0 CA B:ASP57 4.9 29.8 1.0 C B:ASN62 5.0 27.1 1.0 N B:SER67 5.0 33.2 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