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Sodium in PDB 3tkj: Crystal Structure of Human Asparaginase-Like Protein 1 THR168ALA

Enzymatic activity of Crystal Structure of Human Asparaginase-Like Protein 1 THR168ALA

All present enzymatic activity of Crystal Structure of Human Asparaginase-Like Protein 1 THR168ALA:
3.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Asparaginase-Like Protein 1 THR168ALA, PDB code: 3tkj was solved by W.Z.Li, S.D.Yogesha, J.Liu, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.62 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 111.682, 111.371, 119.500, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Asparaginase-Like Protein 1 THR168ALA (pdb code 3tkj). 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 Asparaginase-Like Protein 1 THR168ALA, PDB code: 3tkj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3tkj

Go back to Sodium Binding Sites List in 3tkj
Sodium binding site 1 out of 2 in the Crystal Structure of Human Asparaginase-Like Protein 1 THR168ALA


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 Asparaginase-Like Protein 1 THR168ALA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:32.6
occ:1.00
O A:CYS65 2.2 37.3 1.0
O A:ASP58 2.2 35.2 1.0
O A:ALA63 2.3 33.1 1.0
O A:LEU55 2.5 34.2 1.0
O A:GLU56 2.6 34.9 1.0
O A:PHE61 2.7 32.6 1.0
C A:GLU56 3.2 33.9 1.0
C A:ASP58 3.2 35.2 1.0
C A:CYS65 3.4 38.8 1.0
C A:ALA63 3.5 32.6 1.0
CA A:GLU56 3.5 28.6 1.0
C A:LEU55 3.6 33.1 1.0
C A:PHE61 3.7 33.6 1.0
N A:ASP58 3.8 30.4 1.0
N A:CYS65 3.9 35.1 1.0
N A:GLU56 4.0 29.6 1.0
CA A:ASP58 4.0 30.6 1.0
N A:ALA63 4.1 28.8 1.0
N A:PHE61 4.1 31.5 1.0
CB A:PHE61 4.1 29.5 1.0
CA A:PHE61 4.1 29.5 1.0
N A:PRO59 4.2 32.2 1.0
N A:ASP57 4.2 30.2 1.0
CA A:CYS65 4.2 36.1 1.0
N A:GLY66 4.3 35.4 1.0
C A:GLY64 4.3 36.9 1.0
CA A:PRO59 4.3 32.3 1.0
CA A:ALA63 4.3 27.5 1.0
C A:ASP57 4.3 34.5 1.0
CA A:GLY66 4.4 35.0 1.0
N A:GLY64 4.5 28.9 1.0
CA A:GLY64 4.6 29.1 1.0
CB A:ASP58 4.6 31.1 1.0
CB A:ALA63 4.6 27.1 1.0
C A:PRO59 4.6 38.1 1.0
CB A:CYS65 4.7 37.6 1.0
O A:GLY64 4.7 37.2 1.0
CA A:ASP57 4.7 30.8 1.0
N A:ASN62 4.8 30.6 1.0
CA A:LEU55 4.9 27.5 1.0
C A:GLY66 4.9 38.2 1.0
CB A:GLU56 4.9 28.5 1.0
O A:ASP57 4.9 34.8 1.0
N A:GLU60 5.0 33.9 1.0

Sodium binding site 2 out of 2 in 3tkj

Go back to Sodium Binding Sites List in 3tkj
Sodium binding site 2 out of 2 in the Crystal Structure of Human Asparaginase-Like Protein 1 THR168ALA


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 Asparaginase-Like Protein 1 THR168ALA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:35.0
occ:1.00
O B:CYS65 2.2 36.2 1.0
O B:ALA63 2.2 31.6 1.0
O B:ASP58 2.3 34.4 1.0
O B:LEU55 2.5 33.2 1.0
O B:GLU56 2.6 32.3 1.0
O B:PHE61 2.7 31.8 1.0
C B:GLU56 3.2 32.9 1.0
C B:ASP58 3.3 36.1 1.0
C B:CYS65 3.3 37.7 1.0
C B:ALA63 3.4 32.5 1.0
CA B:GLU56 3.5 28.4 1.0
C B:LEU55 3.6 31.7 1.0
C B:PHE61 3.6 32.0 1.0
N B:ASP58 3.8 31.9 1.0
N B:CYS65 3.9 33.1 1.0
N B:ALA63 4.0 27.3 1.0
N B:GLU56 4.0 28.6 1.0
N B:PHE61 4.1 27.9 1.0
CB B:PHE61 4.1 27.5 1.0
CA B:PHE61 4.1 27.0 1.0
CA B:ASP58 4.1 31.9 1.0
CA B:CYS65 4.2 33.7 1.0
N B:ASP57 4.2 31.1 1.0
CA B:ALA63 4.2 26.8 1.0
C B:GLY64 4.2 36.2 1.0
N B:PRO59 4.2 34.6 1.0
N B:GLY66 4.2 34.1 1.0
CA B:PRO59 4.3 34.7 1.0
CA B:GLY66 4.4 32.9 1.0
C B:ASP57 4.4 35.6 1.0
N B:GLY64 4.4 30.6 1.0
CB B:ALA63 4.6 26.6 1.0
CA B:GLY64 4.6 31.1 1.0
C B:PRO59 4.7 38.5 1.0
O B:GLY64 4.7 35.5 1.0
CB B:ASP58 4.7 32.9 1.0
CB B:CYS65 4.7 34.4 1.0
N B:ASN62 4.7 29.2 1.0
CA B:ASP57 4.8 32.2 1.0
C B:GLY66 4.9 35.0 1.0
CB B:GLU56 4.9 29.4 1.0
CA B:LEU55 4.9 26.0 1.0

Reference:

W.Li, J.R.Cantor, S.D.Yogesha, S.Yang, L.Chantranupong, J.Q.Liu, G.Agnello, G.Georgiou, E.M.Stone, Y.Zhang. Uncoupling Intramolecular Processing and Substrate Hydrolysis in the N-Terminal Nucleophile Hydrolase HASRGL1 By Circular Permutation. Acs Chem.Biol. V. 7 1840 2012.
ISSN: ISSN 1554-8929
PubMed: 22891768
DOI: 10.1021/CB300232N
Page generated: Tue Dec 15 06:26:20 2020

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