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Sodium in PDB 4o0h: Crystal Structure of Human L-Asparaginase Protein with Covalently Linked Substrate L-Asparagine

Enzymatic activity of Crystal Structure of Human L-Asparaginase Protein with Covalently Linked Substrate L-Asparagine

All present enzymatic activity of Crystal Structure of Human L-Asparaginase Protein with Covalently Linked Substrate L-Asparagine:
3.4.19.5; 3.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Human L-Asparaginase Protein with Covalently Linked Substrate L-Asparagine, PDB code: 4o0h 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) 29.83 / 1.97
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 59.651, 59.651, 298.517, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 23.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human L-Asparaginase Protein with Covalently Linked Substrate L-Asparagine (pdb code 4o0h). 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 Human L-Asparaginase Protein with Covalently Linked Substrate L-Asparagine, PDB code: 4o0h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4o0h

Go back to Sodium Binding Sites List in 4o0h
Sodium binding site 1 out of 2 in the Crystal Structure of Human L-Asparaginase Protein with Covalently Linked Substrate L-Asparagine


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 Human L-Asparaginase Protein with Covalently Linked Substrate L-Asparagine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:25.9
occ:1.00
O A:ALA63 2.3 22.8 1.0
O A:ASP58 2.3 23.4 1.0
O A:CYS65 2.3 23.3 1.0
O A:PHE61 2.3 28.1 1.0
O A:LEU55 2.3 23.7 1.0
O A:GLU56 3.2 19.1 1.0
C A:PHE61 3.4 26.6 1.0
C A:ASP58 3.4 26.6 1.0
C A:ALA63 3.4 20.9 1.0
C A:CYS65 3.4 21.6 1.0
C A:LEU55 3.5 23.0 1.0
C A:GLU56 3.6 21.0 1.0
CA A:GLU56 3.8 20.5 1.0
N A:PHE61 3.9 30.3 1.0
CA A:PHE61 3.9 28.6 1.0
CB A:PHE61 4.0 29.0 1.0
N A:ALA63 4.0 20.4 1.0
N A:CYS65 4.0 22.8 1.0
N A:GLU56 4.1 20.4 1.0
CA A:ALA63 4.2 21.8 1.0
N A:ASP58 4.3 23.2 1.0
N A:PRO59 4.3 28.0 1.0
CA A:CYS65 4.3 23.4 1.0
CA A:ASP58 4.3 24.3 1.0
N A:GLY66 4.4 20.9 1.0
CA A:PRO59 4.4 28.8 1.0
N A:GLY64 4.4 21.4 1.0
CA A:GLY66 4.5 20.2 1.0
C A:PRO59 4.5 29.2 1.0
N A:ASN62 4.5 24.8 1.0
N A:ASP57 4.5 21.1 1.0
C A:GLY64 4.6 23.6 1.0
C A:ASP57 4.6 24.1 1.0
CB A:ALA63 4.6 18.8 1.0
CA A:GLY64 4.7 21.6 1.0
C A:GLY66 4.7 20.6 1.0
O A:PRO59 4.7 29.2 1.0
CA A:LEU55 4.8 24.3 1.0
C A:ASN62 4.8 21.6 1.0
N A:GLU60 4.9 31.2 1.0
CB A:ASP58 4.9 24.5 1.0
CB A:CYS65 5.0 23.3 1.0
O A:ASP57 5.0 25.1 1.0

Sodium binding site 2 out of 2 in 4o0h

Go back to Sodium Binding Sites List in 4o0h
Sodium binding site 2 out of 2 in the Crystal Structure of Human L-Asparaginase Protein with Covalently Linked Substrate L-Asparagine


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 Human L-Asparaginase Protein with Covalently Linked Substrate L-Asparagine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:26.7
occ:1.00
O B:CYS65 2.3 26.9 1.0
O B:GLU56 2.3 26.6 1.0
O B:ASP58 2.3 25.6 1.0
O B:ALA63 2.3 24.3 1.0
O B:LEU55 2.3 23.8 1.0
O B:PHE61 2.3 25.5 1.0
C B:GLU56 3.0 28.0 1.0
C B:ASP58 3.2 25.6 1.0
C B:CYS65 3.3 26.2 1.0
CA B:GLU56 3.3 26.4 1.0
C B:PHE61 3.4 22.5 1.0
C B:LEU55 3.4 24.4 1.0
C B:ALA63 3.5 21.6 1.0
N B:ASP58 3.7 24.4 1.0
N B:GLU56 3.8 24.5 1.0
N B:CYS65 3.9 26.2 1.0
CB B:PHE61 3.9 22.2 1.0
N B:ALA63 3.9 21.0 1.0
CA B:PHE61 4.0 23.1 1.0
N B:ASP57 4.0 28.0 1.0
N B:PHE61 4.1 24.9 1.0
CA B:ASP58 4.1 23.9 1.0
N B:PRO59 4.1 27.0 1.0
C B:GLY64 4.1 25.3 1.0
CA B:CYS65 4.1 25.9 1.0
N B:GLY66 4.2 26.5 1.0
CA B:PRO59 4.3 28.5 1.0
CA B:ALA63 4.3 21.4 1.0
CA B:GLY66 4.4 27.0 1.0
N B:GLY64 4.4 22.1 1.0
C B:ASP57 4.4 26.1 1.0
O B:GLY64 4.5 24.6 1.0
N B:ASN62 4.5 21.7 1.0
CA B:GLY64 4.6 24.9 1.0
CB B:ASP58 4.7 21.5 1.0
CB B:ALA63 4.7 18.2 1.0
CB B:GLU56 4.7 26.3 1.0
CA B:ASP57 4.7 26.7 1.0
CB B:CYS65 4.8 28.7 1.0
CA B:LEU55 4.8 24.9 1.0
C B:PRO59 4.8 29.5 1.0
C B:GLY66 4.9 28.1 1.0
C B:ASN62 5.0 21.4 1.0

Reference:

J.Nomme, Y.Su, A.Lavie. Elucidation of the Specific Function of the Conserved Threonine Triad Responsible For Human L-Asparaginase Autocleavage and Substrate Hydrolysis. J.Mol.Biol. V. 426 2471 2014.
ISSN: ISSN 0022-2836
PubMed: 24768817
DOI: 10.1016/J.JMB.2014.04.016
Page generated: Tue Dec 15 06:56:18 2020

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