Sodium in PDB 4pvq: Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein

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

The structure of Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein, PDB code: 4pvq 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 / 2.13
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.220, 59.220, 298.500, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 22.2

The structure of Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein also contains other interesting chemical elements:

Iodine

(I)

4 atoms

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

Sodium binding site 1 out of 2 in the Crystal Structure of Sulfate-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 Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:30.2 occ:1.00 O A:ASP58 2.3 30.1 1.0 O A:CYS65 2.3 30.9 1.0 O A:ALA63 2.3 26.8 1.0 O A:LEU55 2.4 26.6 1.0 O A:PHE61 2.6 27.9 1.0 O A:GLU56 2.9 28.9 1.0 C A:ASP58 3.3 30.6 1.0 C A:GLU56 3.4 28.6 1.0 C A:CYS65 3.5 30.7 1.0 C A:LEU55 3.5 26.4 1.0 C A:ALA63 3.5 26.8 1.0 CA A:GLU56 3.6 27.7 1.0 C A:PHE61 3.6 27.7 1.0 N A:PHE61 3.8 28.4 1.0 N A:CYS65 3.9 30.1 1.0 N A:ALA63 3.9 26.1 1.0 N A:GLU56 4.0 26.3 1.0 N A:ASP58 4.0 30.1 1.0 CA A:PHE61 4.0 28.1 1.0 CB A:PHE61 4.1 28.0 1.0 N A:PRO59 4.1 30.7 1.0 CA A:ASP58 4.2 30.5 1.0 CA A:PRO59 4.2 30.3 1.0 CA A:CYS65 4.2 30.8 1.0 C A:GLY64 4.3 29.2 1.0 CA A:ALA63 4.3 26.6 1.0 N A:ASP57 4.4 28.9 1.0 C A:PRO59 4.4 30.4 1.0 N A:GLY64 4.5 27.5 1.0 N A:GLU60 4.5 30.2 1.0 N A:GLY66 4.5 30.2 1.0 C A:ASP57 4.6 29.7 1.0 CA A:GLY64 4.6 28.5 1.0 CB A:CYS65 4.7 30.9 1.0 N A:ASN62 4.7 26.9 1.0 CA A:GLY66 4.7 29.9 1.0 CB A:ALA63 4.8 26.1 1.0 CB A:ASP58 4.8 30.6 1.0 CA A:LEU55 4.8 26.1 1.0 O A:GLY64 4.9 28.8 1.0 CB A:GLU56 5.0 27.5 1.0 C A:GLU60 5.0 29.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sulfate-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 Crystal Structure of Sulfate-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:24.6 occ:1.00 O B:CYS65 2.2 34.5 1.0 O B:ALA63 2.5 30.2 1.0 O B:PHE61 2.5 29.7 1.0 O B:ASP58 2.6 32.7 1.0 O B:GLU56 2.8 28.3 1.0 O B:LEU55 2.8 24.4 1.0 C B:CYS65 3.3 33.7 1.0 C B:GLU56 3.4 27.9 1.0 C B:ASP58 3.5 32.7 1.0 C B:PHE61 3.6 30.4 1.0 C B:ALA63 3.6 30.2 1.0 CA B:GLU56 3.7 26.4 1.0 C B:LEU55 3.9 24.2 1.0 N B:ALA63 4.0 29.9 1.0 N B:CYS65 4.0 32.9 1.0 N B:PHE61 4.0 31.2 1.0 CA B:PHE61 4.1 30.8 1.0 CA B:PRO59 4.1 32.5 1.0 CA B:GLY66 4.1 32.5 1.0 N B:GLY66 4.2 33.0 1.0 CB B:PHE61 4.2 30.9 1.0 N B:PRO59 4.2 32.7 1.0 CA B:CYS65 4.2 33.9 1.0 N B:ASP58 4.2 31.7 1.0 N B:GLU56 4.3 25.0 1.0 N B:ASP57 4.3 29.0 1.0 CA B:ALA63 4.3 30.1 1.0 C B:PRO59 4.3 32.6 1.0 C B:GLY64 4.4 32.0 1.0 CA B:ASP58 4.5 32.4 1.0 C B:ASP57 4.5 30.9 1.0 O B:PRO59 4.5 32.5 1.0 C B:GLY66 4.5 31.9 1.0 N B:GLY64 4.6 30.4 1.0 CB B:ALA63 4.7 29.5 1.0 N B:ASN62 4.7 29.9 1.0 CA B:GLY64 4.8 31.4 1.0 CA B:ASP57 4.9 30.2 1.0 CB B:CYS65 4.9 34.1 1.0 N B:GLU60 4.9 32.4 1.0 N B:SER67 4.9 31.6 1.0 C B:ASN62 4.9 30.0 1.0 O B:GLY64 5.0 31.8 1.0 O B:ASP57 5.0 31.4 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