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Sodium in PDB 6nrz: Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine

Enzymatic activity of Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine

All present enzymatic activity of Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine:
6.1.1.6;

Protein crystallography data

The structure of Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine, PDB code: 6nrz was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.28 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.170, 57.520, 139.090, 90.00, 96.68, 90.00
R / Rfree (%) 16 / 19.7

Other elements in 6nrz:

The structure of Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine (pdb code 6nrz). 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 Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine, PDB code: 6nrz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6nrz

Go back to Sodium Binding Sites List in 6nrz
Sodium binding site 1 out of 2 in the Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine


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 Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na618

b:52.6
occ:1.00
 O A:LYS463 2.2 37.4 1.0
O A:SER469 2.4 56.3 1.0
O A:HOH969 2.4 41.1 1.0
O A:ASN466 2.5 44.2 1.0
OG A:SER469 2.5 56.8 1.0
O A:HOH987 2.5 64.9 1.0
C A:SER469 3.3 56.3 1.0
C A:LYS463 3.3 38.8 1.0
CB A:SER469 3.6 45.5 1.0
C A:ASN466 3.6 40.5 1.0
CA A:SER469 3.7 49.3 1.0
O A:HOH978 3.8 61.2 1.0
N A:SER469 3.8 51.9 1.0
CA A:ALA464 4.0 31.1 1.0
N A:ALA464 4.1 35.5 1.0
N A:ASN466 4.1 44.5 1.0
C A:ALA464 4.1 33.3 1.0
CA A:ASN466 4.2 39.4 1.0
O A:ALA464 4.3 36.7 1.0
CA A:LYS463 4.3 34.7 1.0
CB A:LYS463 4.4 34.5 1.0
CB A:ASN466 4.4 42.7 1.0
N A:GLU470 4.4 55.9 1.0
N A:PRO467 4.6 41.3 1.0
N A:LEU465 4.7 38.1 1.0
CA A:PRO467 4.8 45.2 1.0
O A:HOH796 4.8 36.4 1.0
C A:GLU470 4.8 45.5 1.0
CA A:GLU470 4.8 53.3 1.0
C A:PRO467 4.9 45.6 1.0
O A:HOH819 4.9 67.3 1.0
CG A:ASN466 5.0 52.7 1.0
N A:ASP468 5.0 34.7 1.0

Sodium binding site 2 out of 2 in 6nrz

Go back to Sodium Binding Sites List in 6nrz
Sodium binding site 2 out of 2 in the Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine


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 Lysyl-Trna Synthetase From Chlamydia Trachomatis Complexed with L-Lysine and Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na619

b:76.6
occ:1.00
 O A:HOH1004 2.4 64.1 1.0
O A:HOH972 2.5 74.4 1.0
O A:GLU368 2.6 52.8 1.0
O A:THR371 2.7 44.9 1.0
O A:HOH719 2.7 48.0 1.0
C A:GLU368 3.7 49.6 1.0
C A:THR371 3.9 42.5 1.0
CA A:SER372 4.1 53.2 1.0
N A:SER372 4.5 42.6 1.0
CA A:GLU368 4.5 42.6 1.0
O A:LEU367 4.6 50.2 1.0
O A:LEU373 4.7 44.3 1.0
N A:THR369 4.7 45.9 1.0
C A:SER372 4.7 52.5 1.0
CA A:THR369 4.9 49.0 1.0
N A:THR371 5.0 41.7 1.0

Reference:

D.M.Dranow, J.Abendroth, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with Complexed with L-Lysine and Adenosine To Be Published.
Page generated: Mon Aug 18 06:18:32 2025

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