Sodium in PDB 4pvs: Crystal Structure of Fully-Cleaved Human L-Asparaginase Protein in Complex with L-Aspartate

All present enzymatic activity of Crystal Structure of Fully-Cleaved Human L-Asparaginase Protein in Complex with L-Aspartate:
3.4.19.5; 3.5.1.1;

The structure of Crystal Structure of Fully-Cleaved Human L-Asparaginase Protein in Complex with L-Aspartate, PDB code: 4pvs 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)	30.00 / 1.84
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.670, 59.670, 298.719, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 21.6

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

Sodium binding site 1 out of 2 in the Crystal Structure of Fully-Cleaved Human L-Asparaginase Protein 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 Fully-Cleaved Human L-Asparaginase Protein in Complex with L-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:21.8 occ:1.00 O A:ALA63 2.2 22.6 1.0 O A:ASP58 2.2 25.4 1.0 O A:CYS65 2.3 26.3 1.0 O A:GLU56 2.6 25.0 1.0 O A:LEU55 2.7 24.8 1.0 O A:PHE61 2.7 24.4 1.0 C A:ASP58 3.3 25.4 1.0 C A:GLU56 3.3 25.2 1.0 C A:CYS65 3.4 26.4 1.0 C A:ALA63 3.4 23.2 1.0 C A:PHE61 3.7 24.3 1.0 CA A:GLU56 3.7 24.9 1.0 C A:LEU55 3.8 24.8 1.0 N A:CYS65 3.9 26.1 1.0 N A:ASP58 3.9 24.8 1.0 N A:ALA63 4.0 22.9 1.0 N A:PHE61 4.0 25.1 1.0 CA A:PHE61 4.1 24.6 1.0 CA A:ASP58 4.2 25.2 1.0 CA A:CYS65 4.2 26.5 1.0 CB A:PHE61 4.2 24.5 1.0 N A:PRO59 4.2 25.8 1.0 N A:GLU56 4.2 24.9 1.0 CA A:ALA63 4.2 23.1 1.0 CA A:PRO59 4.3 26.1 1.0 C A:GLY64 4.3 25.3 1.0 C A:ASP57 4.3 25.1 1.0 N A:ASP57 4.4 24.9 1.0 N A:GLY66 4.4 26.4 1.0 N A:GLY64 4.4 23.8 1.0 CA A:GLY66 4.5 26.8 1.0 C A:PRO59 4.5 26.0 1.0 CA A:GLY64 4.6 24.7 1.0 CB A:ASP58 4.6 25.1 1.0 CB A:CYS65 4.6 26.6 1.0 CB A:ALA63 4.7 22.6 1.0 N A:ASN62 4.8 24.1 1.0 C A:GLY66 4.8 26.8 1.0 O A:ASP57 4.8 25.1 1.0 O A:PRO59 4.8 26.7 1.0 CA A:ASP57 4.9 25.1 1.0 N A:GLU60 4.9 26.0 1.0 O A:GLY64 5.0 25.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Fully-Cleaved Human L-Asparaginase Protein 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 Fully-Cleaved Human L-Asparaginase Protein in Complex with L-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:43.6 occ:1.00 O B:CYS65 2.2 26.8 1.0 O B:ASP58 2.4 24.0 1.0 O B:ALA63 2.4 23.8 1.0 O B:PHE61 2.6 23.9 1.0 O B:GLU56 2.6 24.0 1.0 O B:LEU55 2.8 24.1 1.0 C B:ASP58 3.3 24.5 1.0 C B:CYS65 3.3 26.9 1.0 C B:GLU56 3.4 24.4 1.0 C B:ALA63 3.6 23.6 1.0 C B:PHE61 3.6 23.7 1.0 CA B:GLU56 3.8 24.1 1.0 N B:ASP58 3.9 24.7 1.0 C B:LEU55 3.9 23.9 1.0 N B:CYS65 3.9 26.5 1.0 N B:ALA63 4.0 23.4 1.0 N B:PHE61 4.0 24.0 1.0 CA B:PHE61 4.1 24.0 1.0 CB B:PHE61 4.1 24.6 1.0 N B:PRO59 4.1 24.4 1.0 CA B:CYS65 4.1 27.1 1.0 CA B:ASP58 4.2 24.5 1.0 CA B:PRO59 4.2 24.4 1.0 C B:GLY64 4.2 25.5 1.0 N B:GLY66 4.3 26.8 1.0 N B:GLU56 4.3 23.8 1.0 N B:ASP57 4.4 24.7 1.0 CA B:ALA63 4.4 23.5 1.0 C B:ASP57 4.4 24.8 1.0 CA B:GLY66 4.4 27.0 1.0 N B:GLY64 4.5 23.9 1.0 C B:PRO59 4.5 24.4 1.0 O B:GLY64 4.6 25.2 1.0 CA B:GLY64 4.6 24.7 1.0 CB B:CYS65 4.6 27.3 1.0 N B:ASN62 4.8 23.6 1.0 C B:GLY66 4.8 27.0 1.0 CB B:ALA63 4.8 23.4 1.0 CB B:ASP58 4.8 24.8 1.0 CA B:ASP57 4.9 25.1 1.0 N B:GLU60 4.9 24.4 1.0

J.Nomme, Y.Su, M.Konrad, A.Lavie. Structures of Apo and Product-Bound Human L-Asparaginase: Insights Into the Mechanism of Autoproteolysis and Substrate Hydrolysis. Biochemistry V. 51 6816 2012.
ISSN: ISSN 0006-2960
PubMed: 22861376
DOI: 10.1021/BI300870G