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

Protein crystallography data

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

Other elements in 8sbm:

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

Sodium Binding Sites:

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 8sbm

Go back to Sodium Binding Sites List in 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

Reference:

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
Page generated: Thu Dec 28 11:44:41 2023

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