Sodium in PDB 4o48: Crystal Structure of Cleaved Guinea Pig L-Asparaginase Type III in Complex with L-Aspartate

All present enzymatic activity of Crystal Structure of Cleaved Guinea Pig L-Asparaginase Type III in Complex with L-Aspartate:
3.5.1.1;

The structure of Crystal Structure of Cleaved Guinea Pig L-Asparaginase Type III in Complex with L-Aspartate, PDB code: 4o48 was solved by A.M.Schalk, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.65 / 2.29
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.580, 114.580, 138.590, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.1

The binding sites of Sodium atom in the Crystal Structure of Cleaved Guinea Pig L-Asparaginase Type III in Complex with L-Aspartate (pdb code 4o48). 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 Cleaved Guinea Pig L-Asparaginase Type III in Complex with L-Aspartate, PDB code: 4o48:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Cleaved Guinea Pig L-Asparaginase Type III in Complex with L-Aspartate


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 Cleaved Guinea Pig L-Asparaginase Type III in Complex with L-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:30.7 occ:1.00 O A:ALA63 2.2 27.3 1.0 O A:ASP58 2.3 33.8 1.0 O A:HIS65 2.3 36.3 1.0 O A:GLU56 2.5 32.9 1.0 O A:PHE61 2.7 26.7 1.0 O A:LEU55 2.8 32.8 1.0 C A:GLU56 3.2 30.5 1.0 C A:ASP58 3.4 34.7 1.0 C A:ALA63 3.4 26.9 1.0 C A:HIS65 3.4 30.4 1.0 CA A:GLU56 3.5 29.1 1.0 C A:PHE61 3.7 29.2 1.0 C A:LEU55 3.8 31.3 1.0 N A:HIS65 4.0 26.1 1.0 CA A:ALA59 4.0 28.9 1.0 N A:ALA63 4.0 28.1 1.0 N A:ALA59 4.1 34.2 1.0 N A:GLU56 4.1 29.2 1.0 N A:PHE61 4.2 33.4 1.0 N A:ASP58 4.2 32.7 1.0 C A:GLY64 4.2 26.8 1.0 CB A:PHE61 4.2 27.4 1.0 N A:ASP57 4.2 30.4 1.0 CA A:PHE61 4.3 28.5 1.0 CA A:HIS65 4.3 27.9 1.0 N A:GLY66 4.3 31.5 1.0 CA A:ALA63 4.3 28.7 1.0 CA A:ASP58 4.3 31.3 1.0 N A:GLY64 4.3 25.9 1.0 C A:ASP57 4.4 32.2 1.0 C A:ALA59 4.4 29.3 1.0 CA A:GLY66 4.4 32.9 1.0 CA A:GLY64 4.5 26.9 1.0 O A:GLY64 4.7 30.4 1.0 CB A:ALA63 4.7 28.9 1.0 O A:ALA59 4.7 26.8 1.0 CB A:HIS65 4.7 29.1 1.0 CA A:ASP57 4.7 31.0 1.0 O A:ASP57 4.8 32.8 1.0 C A:GLY66 4.8 31.5 1.0 N A:ASN62 4.8 28.3 1.0 CB A:GLU56 4.9 28.5 1.0 N A:GLU60 4.9 31.7 1.0 CB A:ASP58 4.9 34.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Cleaved Guinea Pig L-Asparaginase Type III in Complex with L-Aspartate


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 Cleaved Guinea Pig L-Asparaginase Type III in Complex with L-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:36.2 occ:1.00 O B:HIS65 2.2 24.6 1.0 O B:ALA63 2.3 34.2 1.0 O B:ASP58 2.3 36.5 1.0 O B:GLU56 2.4 36.5 1.0 O B:PHE61 2.7 30.4 1.0 O B:LEU55 2.7 35.0 1.0 C B:GLU56 3.1 32.9 1.0 C B:HIS65 3.4 28.4 1.0 C B:ASP58 3.4 38.6 1.0 C B:ALA63 3.4 32.5 1.0 CA B:GLU56 3.5 32.0 1.0 C B:PHE61 3.6 36.5 1.0 N B:ALA63 3.8 36.6 1.0 C B:LEU55 3.8 31.3 1.0 CB B:PHE61 4.0 39.5 1.0 N B:HIS65 4.0 22.5 1.0 N B:ASP58 4.0 38.9 1.0 CA B:PHE61 4.1 41.1 1.0 N B:PHE61 4.1 46.9 1.0 CA B:ALA63 4.1 33.5 1.0 N B:GLU56 4.2 31.6 1.0 C B:GLY64 4.2 23.4 1.0 N B:GLY66 4.2 33.4 1.0 N B:ASP57 4.3 34.5 1.0 CA B:GLY66 4.3 38.0 1.0 CA B:HIS65 4.3 25.9 1.0 CA B:ASP58 4.3 37.7 1.0 N B:ALA59 4.3 37.2 1.0 CB B:ALA63 4.4 32.3 1.0 CA B:ALA59 4.4 40.0 1.0 N B:GLY64 4.4 31.3 1.0 C B:ASP57 4.5 38.8 1.0 CA B:GLY64 4.5 25.7 1.0 N B:ASN62 4.6 36.0 1.0 O B:GLY64 4.7 20.0 1.0 CB B:HIS65 4.7 27.9 1.0 C B:ALA59 4.8 43.4 1.0 CB B:GLU56 4.8 30.8 1.0 CB B:ASP58 4.8 38.9 1.0 C B:GLY66 4.8 42.3 1.0 CA B:ASP57 4.8 35.6 1.0 C B:ASN62 4.9 38.0 1.0

A.M.Schalk, A.Lavie. Structural and Kinetic Characterization of Guinea Pig L-Asparaginase Type III. Biochemistry V. 53 2318 2014.
ISSN: ISSN 0006-2960
PubMed: 24669941
DOI: 10.1021/BI401692V