Atomistry » Sodium » PDB 4nxz-4obo » 4o0c
Atomistry »
  Sodium »
    PDB 4nxz-4obo »
      4o0c »

Sodium in PDB 4o0c: High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein

Enzymatic activity of High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein

All present enzymatic activity of High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein:
3.4.19.5; 3.5.1.1;

Protein crystallography data

The structure of High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein, PDB code: 4o0c 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) 29.04 / 1.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 59.213, 59.213, 297.793, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 20.5

Other elements in 4o0c:

The structure of High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein (pdb code 4o0c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein, PDB code: 4o0c:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4o0c

Go back to Sodium Binding Sites List in 4o0c
Sodium binding site 1 out of 5 in the High Resolution Crystal Structure of Uncleaved 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 High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:16.0
occ:1.00
 O A:ALA63 2.3 14.3 1.0
O A:ASP58 2.4 17.1 1.0
O A:CYS65 2.4 16.6 1.0
O A:GLU56 2.5 17.4 1.0
O A:LEU55 2.6 15.4 1.0
O A:PHE61 2.7 14.7 1.0
C A:GLU56 3.2 13.1 1.0
C A:ASP58 3.3 16.0 1.0
C A:CYS65 3.5 14.9 1.0
C A:ALA63 3.5 13.9 1.0
CA A:GLU56 3.6 13.8 1.0
C A:PHE61 3.7 13.5 1.0
C A:LEU55 3.7 13.2 1.0
N A:ASP58 3.9 16.5 1.0
N A:PHE61 4.0 15.2 1.0
CB A:PHE61 4.0 16.5 1.0
N A:PRO59 4.1 18.5 1.0
N A:ALA63 4.1 14.9 1.0
CA A:PHE61 4.1 15.1 1.0
N A:GLU56 4.1 13.3 1.0
CA A:PRO59 4.2 18.7 1.0
N A:CYS65 4.2 16.4 1.0
CA A:ASP58 4.2 15.0 1.0
N A:ASP57 4.2 15.2 1.0
CA A:ALA63 4.3 13.1 1.0
N A:GLY66 4.3 14.4 1.0
CA A:GLY66 4.3 15.5 1.0
C A:GLY64 4.3 15.5 1.0
CA A:CYS65 4.3 14.6 1.0
C A:ASP57 4.5 16.3 1.0
N A:GLY64 4.5 13.2 1.0
C A:PRO59 4.5 16.3 1.0
CB A:ALA63 4.6 12.7 1.0
CA A:GLY64 4.7 15.5 1.0
O A:GLY64 4.7 16.2 1.0
CB A:ASP58 4.8 16.0 1.0
C A:GLY66 4.8 16.6 1.0
CA A:ASP57 4.8 16.9 1.0
N A:ASN62 4.8 12.8 1.0
CB A:CYS65 4.9 14.1 1.0
N A:GLU60 4.9 16.2 1.0
N A:SER67 4.9 18.5 1.0
O A:PRO59 5.0 19.0 1.0
CB A:GLU56 5.0 12.1 1.0

Sodium binding site 2 out of 5 in 4o0c

Go back to Sodium Binding Sites List in 4o0c
Sodium binding site 2 out of 5 in the High Resolution Crystal Structure of Uncleaved 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 High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:20.8
occ:1.00
 O A:HOH646 2.8 21.3 1.0
O A:HOH639 3.0 17.2 1.0
N A:GLY10 3.4 14.9 1.0
CD2 A:PHE61 3.8 15.4 1.0
CG A:PRO284 4.0 16.4 1.0
CE2 A:PHE61 4.0 14.9 1.0
CA A:GLY9 4.0 17.6 1.0
C A:GLY9 4.2 16.4 1.0
CA A:GLY10 4.2 14.8 1.0
CD A:PRO284 4.4 14.7 1.0
NH2 A:ARG19 4.6 23.1 1.0
O A:GLY10 4.7 16.0 1.0
CB A:PRO284 4.7 15.2 1.0
CG A:PHE61 4.9 16.2 1.0
O A:GLU60 4.9 17.9 1.0
O A:GLY167 4.9 19.5 1.0

Sodium binding site 3 out of 5 in 4o0c

Go back to Sodium Binding Sites List in 4o0c
Sodium binding site 3 out of 5 in the High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:16.7
occ:1.00
 O B:CYS65 2.2 16.8 1.0
O B:ALA63 2.2 16.8 1.0
O B:ASP58 2.3 17.6 1.0
O B:LEU55 2.4 15.5 1.0
O B:GLU56 2.5 16.4 1.0
O B:PHE61 2.6 19.6 1.0
C B:GLU56 3.2 15.5 1.0
C B:CYS65 3.3 17.1 1.0
C B:ASP58 3.3 15.4 1.0
C B:ALA63 3.5 15.2 1.0
C B:LEU55 3.5 13.7 1.0
CA B:GLU56 3.5 11.6 1.0
C B:PHE61 3.6 16.4 1.0
N B:CYS65 3.7 18.0 1.0
N B:ALA63 3.9 14.9 1.0
N B:ASP58 3.9 14.5 1.0
N B:GLU56 3.9 12.4 1.0
CA B:CYS65 4.0 17.2 1.0
CB B:PHE61 4.1 17.7 1.0
C B:GLY64 4.1 15.3 1.0
CA B:ASP58 4.1 14.1 1.0
CA B:PHE61 4.1 17.1 1.0
N B:PHE61 4.2 18.4 1.0
CA B:PRO59 4.2 17.2 1.0
N B:ASP57 4.2 14.8 1.0
C B:ASP57 4.2 14.6 1.0
N B:PRO59 4.3 16.8 1.0
CA B:ALA63 4.3 14.3 1.0
N B:GLY66 4.3 16.7 1.0
N B:GLY64 4.4 14.0 1.0
CA B:GLY66 4.5 18.0 1.0
CA B:GLY64 4.5 15.9 1.0
CB B:CYS65 4.5 18.8 1.0
C B:PRO59 4.6 16.8 1.0
CB B:ASP58 4.7 15.0 1.0
N B:ASN62 4.7 15.0 1.0
O B:ASP57 4.7 17.5 1.0
CA B:ASP57 4.7 15.1 1.0
O B:GLY64 4.7 15.7 1.0
CA B:LEU55 4.8 14.1 1.0
CB B:ALA63 4.8 17.5 1.0
C B:GLY66 4.9 16.6 1.0
O B:PRO59 4.9 17.3 1.0
CB B:GLU56 4.9 14.4 1.0
C B:ASN62 5.0 14.9 1.0
N B:GLU60 5.0 15.9 1.0

Sodium binding site 4 out of 5 in 4o0c

Go back to Sodium Binding Sites List in 4o0c
Sodium binding site 4 out of 5 in the High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:16.2
occ:1.00
 O B:HOH540 2.3 18.6 1.0
O B:MET109 2.4 17.0 1.0
O B:HIS114 2.4 14.6 1.0
O B:THR112 2.5 15.0 1.0
O B:VAL108 2.8 15.0 1.0
C B:MET109 3.2 15.5 1.0
C B:HIS114 3.5 14.6 1.0
CA B:MET109 3.5 15.6 1.0
N B:HIS114 3.6 14.8 1.0
C B:THR112 3.6 16.1 1.0
OG1 B:THR112 3.7 16.5 1.0
C B:VAL108 3.8 14.7 1.0
C B:PRO113 3.9 16.3 1.0
CA B:HIS114 4.1 14.2 1.0
N B:MET109 4.2 14.8 1.0
CA B:PRO113 4.3 15.2 1.0
N B:THR112 4.3 15.3 1.0
N B:GLU110 4.4 15.6 1.0
NA B:NA403 4.4 21.7 1.0
N B:PRO113 4.4 15.0 1.0
CA B:THR112 4.4 14.5 1.0
O B:PRO113 4.4 15.7 1.0
N B:CYS115 4.5 14.3 1.0
O B:ALA89 4.5 13.7 1.0
CB B:THR112 4.7 15.3 1.0
CA B:CYS115 4.8 13.6 1.0
CB B:MET109 4.8 15.7 1.0
O A:HOH664 4.9 23.1 1.0
CG B:MET109 5.0 16.7 1.0

Sodium binding site 5 out of 5 in 4o0c

Go back to Sodium Binding Sites List in 4o0c
Sodium binding site 5 out of 5 in the High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of High Resolution Crystal Structure of Uncleaved Human L-Asparaginase Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:21.7
occ:1.00
 O A:HOH664 2.5 23.1 1.0
O B:HOH540 2.6 18.6 1.0
CA B:SER88 3.5 14.8 1.0
OG B:SER88 3.7 17.0 1.0
CB B:SER88 3.7 16.1 1.0
NZ A:LYS227 3.8 14.9 1.0
CD A:LYS227 3.8 14.2 1.0
N B:ALA89 3.9 14.1 1.0
SG B:CYS115 3.9 18.2 1.0
CE A:LYS227 4.1 15.3 1.0
O B:HOH571 4.1 17.9 1.0
O A:HOH674 4.3 24.8 1.0
C B:SER88 4.3 14.8 1.0
NA B:NA402 4.4 16.2 1.0
O B:ALA89 4.4 13.7 1.0
N B:SER88 4.6 13.4 1.0
CG A:LYS227 4.9 15.5 1.0
O B:LEU87 4.9 12.4 1.0
CG B:MET109 5.0 16.7 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: Mon Oct 7 17:20:43 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy