Sodium in PDB 4pvp: Crystal Structure of Malonate-Bound Human L-Asparaginase Protein

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

The structure of Crystal Structure of Malonate-Bound Human L-Asparaginase Protein, PDB code: 4pvp 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)	29.73 / 1.85
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.459, 59.459, 298.900, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 20.4

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

Sodium binding site 1 out of 2 in the Crystal Structure of Malonate-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 Malonate-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:23.5 occ:1.00 O A:ALA63 2.3 21.4 1.0 O A:ASP58 2.4 23.9 1.0 O A:CYS65 2.4 22.4 1.0 O A:GLU56 2.5 20.6 1.0 O A:LEU55 2.7 20.2 1.0 O A:PHE61 2.8 22.6 1.0 C A:GLU56 3.2 20.8 1.0 C A:ASP58 3.3 24.0 1.0 C A:ALA63 3.5 21.0 1.0 C A:CYS65 3.5 22.3 1.0 CA A:GLU56 3.6 20.1 1.0 C A:PHE61 3.6 22.2 1.0 C A:LEU55 3.7 20.4 1.0 N A:ASP58 3.9 23.2 1.0 N A:PHE61 3.9 23.1 1.0 CB A:PHE61 4.0 22.3 1.0 N A:ALA63 4.0 21.1 1.0 N A:CYS65 4.0 22.2 1.0 CA A:PHE61 4.0 22.7 1.0 N A:PRO59 4.1 24.1 1.0 N A:GLU56 4.1 20.1 1.0 CA A:ASP58 4.2 23.7 1.0 CA A:PRO59 4.2 24.6 1.0 C A:GLY64 4.2 21.6 1.0 N A:ASP57 4.3 21.2 1.0 CA A:CYS65 4.3 22.5 1.0 CA A:ALA63 4.4 21.0 1.0 C A:ASP57 4.4 23.1 1.0 N A:GLY66 4.4 22.6 1.0 N A:GLY64 4.5 21.0 1.0 C A:PRO59 4.5 24.6 1.0 CA A:GLY66 4.5 22.6 1.0 CA A:GLY64 4.6 21.2 1.0 O A:GLY64 4.6 21.6 1.0 N A:ASN62 4.7 21.8 1.0 CB A:ASP58 4.7 23.7 1.0 N A:GLU60 4.8 24.5 1.0 CA A:ASP57 4.8 22.2 1.0 CB A:CYS65 4.8 22.9 1.0 C A:GLY66 4.8 22.8 1.0 CB A:ALA63 4.8 20.5 1.0 O A:ASP57 4.9 23.4 1.0 CB A:GLU56 5.0 19.9 1.0 O A:PRO59 5.0 24.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Malonate-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 Malonate-Bound Human L-Asparaginase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:27.1 occ:1.00 O B:CYS65 2.2 22.2 1.0 O B:ASP58 2.4 21.1 1.0 O B:ALA63 2.4 18.7 1.0 O B:LEU55 2.5 19.2 1.0 O B:PHE61 2.6 18.5 1.0 O B:GLU56 2.8 19.6 1.0 C B:CYS65 3.3 22.4 1.0 C B:GLU56 3.3 19.6 1.0 C B:ASP58 3.3 21.4 1.0 C B:ALA63 3.6 18.5 1.0 C B:LEU55 3.6 19.5 1.0 CA B:GLU56 3.6 19.2 1.0 C B:PHE61 3.6 18.8 1.0 N B:CYS65 3.9 21.8 1.0 N B:ASP58 4.0 21.0 1.0 N B:ALA63 4.0 17.8 1.0 N B:GLU56 4.1 19.4 1.0 N B:PHE61 4.1 20.1 1.0 CA B:CYS65 4.1 22.4 1.0 CA B:PHE61 4.2 19.6 1.0 CB B:PHE61 4.2 19.8 1.0 CA B:ASP58 4.2 21.4 1.0 N B:PRO59 4.2 21.6 1.0 N B:GLY66 4.3 22.5 1.0 N B:ASP57 4.3 19.9 1.0 CA B:PRO59 4.3 21.8 1.0 C B:ASP57 4.4 21.1 1.0 C B:GLY64 4.4 20.9 1.0 CA B:ALA63 4.4 18.3 1.0 CA B:GLY66 4.5 23.1 1.0 N B:GLY64 4.5 18.5 1.0 C B:PRO59 4.6 22.1 1.0 CB B:CYS65 4.6 22.7 1.0 CA B:GLY64 4.7 20.2 1.0 CB B:ALA63 4.8 17.6 1.0 O B:ASP57 4.8 21.5 1.0 N B:ASN62 4.8 17.9 1.0 CB B:ASP58 4.8 21.9 1.0 C B:GLY66 4.9 23.2 1.0 CA B:ASP57 4.9 20.8 1.0 CA B:LEU55 4.9 19.7 1.0 N B:GLU60 4.9 22.0 1.0 O B:PRO59 5.0 22.5 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