Sodium in PDB 8u2q: Crystal Structure of Glycine--Trna Ligase Active Site Chimera From Mycobacterium Thermoresistibile/Tuberculosis (G5A Bound)

The structure of Crystal Structure of Glycine--Trna Ligase Active Site Chimera From Mycobacterium Thermoresistibile/Tuberculosis (G5A Bound), PDB code: 8u2q 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)	41.53 / 2.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.286, 87.388, 99.152, 90, 104.12, 90
R / Rfree (%)	18.5 / 20.9

The structure of Crystal Structure of Glycine--Trna Ligase Active Site Chimera From Mycobacterium Thermoresistibile/Tuberculosis (G5A Bound) also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Glycine--Trna Ligase Active Site Chimera From Mycobacterium Thermoresistibile/Tuberculosis (G5A Bound) (pdb code 8u2q). 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 Glycine--Trna Ligase Active Site Chimera From Mycobacterium Thermoresistibile/Tuberculosis (G5A Bound), PDB code: 8u2q:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Glycine--Trna Ligase Active Site Chimera From Mycobacterium Thermoresistibile/Tuberculosis (G5A Bound)


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 Glycine--Trna Ligase Active Site Chimera From Mycobacterium Thermoresistibile/Tuberculosis (G5A Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:53.6 occ:1.00 O A:ARG57 2.3 49.7 1.0 O A:VAL54 2.3 54.3 1.0 O A:VAL60 2.4 47.4 1.0 C A:VAL54 3.5 45.9 1.0 C A:ARG57 3.5 44.9 1.0 C A:VAL60 3.6 48.6 1.0 O A:HOH656 4.0 51.4 1.0 CA A:VAL54 4.2 49.6 1.0 CG1 A:VAL54 4.3 45.8 1.0 O A:GLU58 4.3 53.1 1.0 N A:VAL60 4.3 49.1 1.0 N A:ARG57 4.4 45.9 1.0 C A:GLU58 4.4 56.6 1.0 N A:GLU58 4.4 50.4 1.0 CA A:GLU58 4.4 53.2 1.0 O A:THR55 4.4 45.0 1.0 CA A:ARG57 4.5 47.8 1.0 N A:THR55 4.5 48.5 1.0 OD1 B:ASN395 4.5 62.1 1.0 CA A:VAL60 4.5 44.0 1.0 N A:VAL61 4.5 46.0 1.0 C A:THR55 4.6 44.9 1.0 CA A:THR55 4.6 47.6 1.0 CA A:VAL61 4.6 48.2 1.0 CG1 A:VAL61 4.8 52.2 1.0 CB A:VAL54 4.9 49.3 1.0 CB A:ARG57 4.9 43.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Glycine--Trna Ligase Active Site Chimera From Mycobacterium Thermoresistibile/Tuberculosis (G5A Bound)


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 Glycine--Trna Ligase Active Site Chimera From Mycobacterium Thermoresistibile/Tuberculosis (G5A Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:52.1 occ:1.00 O B:VAL54 2.2 48.2 1.0 O B:VAL60 2.5 43.1 1.0 O B:ARG57 2.5 49.9 1.0 C B:VAL54 3.3 39.8 1.0 C B:ARG57 3.7 46.6 1.0 C B:VAL60 3.7 44.0 1.0 O B:HOH607 3.7 40.1 1.0 CG1 B:VAL54 4.0 41.1 1.0 CA B:VAL54 4.1 45.1 1.0 O A:HOH631 4.3 52.1 1.0 N B:THR55 4.3 43.0 1.0 OD1 A:ASN395 4.4 51.1 1.0 O B:THR55 4.4 44.9 1.0 CA B:THR55 4.4 45.0 1.0 N B:ARG57 4.5 48.0 1.0 C B:THR55 4.5 45.4 1.0 CA B:VAL61 4.6 43.1 1.0 N B:GLU58 4.6 54.2 1.0 N B:VAL61 4.6 42.0 1.0 CA B:GLU58 4.6 46.0 1.0 N B:VAL60 4.6 41.5 1.0 CA B:ARG57 4.6 42.7 1.0 O B:GLU58 4.7 46.6 1.0 C B:GLU58 4.7 46.0 1.0 CA B:VAL60 4.7 46.4 1.0 CB B:VAL54 4.7 44.0 1.0 CG1 B:VAL61 4.8 42.2 1.0

S.Seibold, S.Lovell, K.P.Battaile, A.Derocher. Crystal Structure of Glycine--Trna Ligase Active Site Chimera From Mycobacterium Thermoresistibile/Tuberculosis (G5A Bound) To Be Published.