Sodium in PDB 8sbm: Crystal Structure of the Wild-Type Catalytic Atp-Binding Domain of Mtb Doss

The structure of Crystal Structure of the Wild-Type Catalytic Atp-Binding Domain of Mtb Doss, PDB code: 8sbm was solved by G.Larson, K.Shi, H.Aihara, A.Bhagi-Damodaran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.60 / 1.47
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	54.438, 61.775, 72.234, 90, 107.54, 90
R / Rfree (%)	15.3 / 19.3

The structure of Crystal Structure of the Wild-Type Catalytic Atp-Binding Domain of Mtb Doss also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of the Wild-Type Catalytic Atp-Binding Domain of Mtb Doss (pdb code 8sbm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Wild-Type Catalytic Atp-Binding Domain of Mtb Doss, PDB code: 8sbm:

Sodium binding site 1 out of 1 in the Crystal Structure of the Wild-Type Catalytic Atp-Binding Domain of Mtb Doss


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 the Wild-Type Catalytic Atp-Binding Domain of Mtb Doss within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:47.1 occ:1.00 O B:ALA565 2.1 28.5 1.0 O B:GLY567 2.5 24.5 1.0 CA B:SER566 2.5 27.6 1.0 C B:SER566 2.6 27.4 1.0 C B:ALA565 2.8 26.8 1.0 N B:SER566 2.9 29.5 1.0 N B:VAL562 3.0 26.1 1.0 N B:GLY567 3.0 24.5 1.0 CB B:SER561 3.1 18.8 1.0 O B:SER566 3.3 28.4 1.0 CA B:SER561 3.5 17.8 1.0 C B:GLY567 3.5 20.0 1.0 CG2 B:VAL562 3.6 24.1 1.0 C B:SER561 3.7 22.1 1.0 O B:VAL562 3.8 27.4 1.0 CA B:GLY567 3.8 21.9 1.0 CB B:SER566 4.0 32.1 1.0 O B:HOH720 4.0 22.8 1.0 CA B:VAL562 4.0 27.7 1.0 OG B:SER561 4.2 19.6 1.0 CA B:ALA565 4.2 31.1 1.0 CB B:VAL562 4.3 27.0 1.0 C B:VAL562 4.4 29.4 1.0 N B:ALA565 4.6 29.8 1.0 N B:THR568 4.7 19.2 1.0 CB B:ALA565 4.8 34.2 1.0 CG1 B:VAL562 4.8 29.2 1.0 N B:SER561 4.9 16.2 1.0 O B:SER561 4.9 25.8 1.0 OG B:SER566 4.9 31.6 1.0

G.W.Larson, P.K.Windsor, E.Smithwick, K.Shi, H.Aihara, A.Rama Damodaran, A.Bhagi-Damodaran. Understanding Atp Binding to Doss Catalytic Domain with A Short Atp-Lid. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 37905955
DOI: 10.1021/ACS.BIOCHEM.3C00306