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

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

The structure of Crystal Structure of Partially-Cleaved Human L-Asparaginase Protein in Complex with L-Aspartate, PDB code: 4pvr 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 / 1.75
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	59.500, 59.500, 299.500, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 19.1

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

Sodium binding site 1 out of 2 in the Crystal Structure of Partially-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 Partially-Cleaved Human L-Asparaginase Protein in Complex with L-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:8.4 occ:1.00 O A:ASP58 2.3 11.7 1.0 O A:CYS65 2.3 12.8 1.0 O A:ALA63 2.4 8.7 1.0 O A:GLU56 2.6 11.1 1.0 O A:PHE61 2.7 12.0 1.0 O A:LEU55 2.7 9.1 1.0 C A:ASP58 3.3 12.5 1.0 C A:GLU56 3.4 10.2 1.0 C A:CYS65 3.4 12.0 1.0 C A:ALA63 3.6 9.0 1.0 C A:PHE61 3.6 11.6 1.0 CA A:GLU56 3.8 9.7 1.0 C A:LEU55 3.8 9.4 1.0 CB A:PHE61 4.0 12.2 1.0 N A:PHE61 4.0 12.6 1.0 N A:ALA63 4.0 9.0 1.0 N A:CYS65 4.0 11.2 1.0 CA A:PHE61 4.0 12.4 1.0 N A:ASP58 4.1 12.3 1.0 N A:PRO59 4.2 12.9 1.0 CA A:PRO59 4.2 13.2 1.0 CA A:CYS65 4.3 12.5 1.0 N A:GLU56 4.3 8.9 1.0 CA A:ASP58 4.3 12.1 1.0 C A:GLY64 4.3 10.3 1.0 N A:GLY66 4.3 12.0 1.0 CA A:GLY66 4.3 11.8 1.0 CA A:ALA63 4.4 9.0 1.0 N A:ASP57 4.4 10.6 1.0 C A:PRO59 4.5 13.6 1.0 C A:ASP57 4.5 12.1 1.0 N A:GLY64 4.5 9.3 1.0 CA A:GLY64 4.7 9.8 1.0 C A:GLY66 4.7 11.6 1.0 N A:ASN62 4.7 11.3 1.0 CB A:ALA63 4.8 9.4 1.0 O A:PRO59 4.8 14.3 1.0 O A:GLY64 4.8 10.2 1.0 CB A:CYS65 4.8 12.9 1.0 N A:GLU60 4.9 13.6 1.0 CA A:ASP57 4.9 11.7 1.0 CB A:ASP58 4.9 12.5 1.0 O A:ASP57 4.9 13.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Partially-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 Partially-Cleaved Human L-Asparaginase Protein in Complex with L-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:13.2 occ:1.00 O B:CYS65 2.1 10.9 1.0 O B:ALA63 2.3 9.2 1.0 O B:ASP58 2.3 10.5 1.0 O B:GLU56 2.4 10.9 1.0 O B:LEU55 2.6 10.0 1.0 O B:PHE61 2.9 10.9 1.0 C B:GLU56 3.1 10.7 1.0 C B:ASP58 3.2 12.3 1.0 C B:CYS65 3.3 11.2 1.0 C B:ALA63 3.5 9.8 1.0 CA B:GLU56 3.6 10.2 1.0 C B:LEU55 3.7 10.0 1.0 N B:ASP58 3.8 12.5 1.0 C B:PHE61 3.8 10.8 1.0 N B:CYS65 3.9 12.1 1.0 N B:ALA63 4.0 9.9 1.0 CA B:ASP58 4.1 12.2 1.0 CA B:CYS65 4.1 12.1 1.0 N B:GLU56 4.1 9.5 1.0 N B:PRO59 4.1 12.7 1.0 N B:ASP57 4.1 11.3 1.0 N B:PHE61 4.1 11.7 1.0 CA B:PRO59 4.2 13.2 1.0 C B:GLY64 4.2 11.4 1.0 C B:ASP57 4.3 12.6 1.0 CB B:PHE61 4.3 11.7 1.0 CA B:PHE61 4.3 11.5 1.0 N B:GLY66 4.3 10.5 1.0 CA B:ALA63 4.3 9.8 1.0 CA B:GLY66 4.5 10.2 1.0 N B:GLY64 4.5 10.6 1.0 C B:PRO59 4.5 13.4 1.0 CB B:CYS65 4.5 12.3 1.0 CA B:GLY64 4.6 10.9 1.0 CB B:ASP58 4.6 13.0 1.0 CA B:ASP57 4.6 12.2 1.0 O B:GLY64 4.8 11.8 1.0 CB B:ALA63 4.8 10.2 1.0 N B:GLU60 4.8 13.4 1.0 O B:ASP57 4.9 13.6 1.0 C B:GLY66 4.9 10.0 1.0 CB B:GLU56 4.9 9.1 1.0 N B:ASN62 5.0 10.7 1.0 CA B:LEU55 5.0 9.8 1.0 O B:PRO59 5.0 14.4 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