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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: Tue Dec 15 06:56:15 2020

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