Zinc 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:

Sodium

(Na)

1 atom

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Wild-Type Catalytic Atp-Binding Domain of Mtb Doss, PDB code: 8sbm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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 A:Zn601 b:34.3 occ:1.00 OD2 A:ASP529 1.9 33.3 1.0 OE2 A:GLU537 2.0 31.7 1.0 NE2 A:HIS507 2.1 35.8 1.0 O A:HOH714 2.1 30.8 1.0 OE1 A:GLU537 2.2 34.2 1.0 CD A:GLU537 2.4 32.2 1.0 CG A:ASP529 2.9 33.3 1.0 CD2 A:HIS507 3.0 39.7 1.0 CE1 A:HIS507 3.0 39.0 1.0 OD1 A:ASP529 3.1 31.9 1.0 O A:VAL505 3.6 34.0 1.0 O A:HOH724 3.9 36.1 1.0 CG A:GLU537 4.0 30.8 1.0 N A:VAL505 4.0 33.1 1.0 ND1 A:HIS507 4.1 40.2 1.0 CG A:HIS507 4.2 39.8 1.0 O A:HOH728 4.2 38.3 1.0 CB A:ASP529 4.2 32.9 1.0 CE2 A:PHE538 4.3 29.2 1.0 CZ A:PHE538 4.3 30.3 1.0 CA A:ALA504 4.4 29.4 1.0 CB A:ALA504 4.5 28.7 1.0 C A:VAL505 4.6 35.3 1.0 O A:HOH733 4.7 45.6 1.0 C A:ALA504 4.7 32.6 1.0 CG2 A:VAL505 4.8 35.3 1.0 CA A:GLY531 4.9 38.4 1.0 CA A:VAL505 4.9 32.7 1.0 CB A:GLU537 4.9 30.5 1.0 CD1 A:LEU534 5.0 38.5 1.0

Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn binding site number 2 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 A:Zn606 b:34.9 occ:0.72 OD1 A:ASP522 2.0 34.3 1.0 O A:HOH745 2.0 43.0 1.0 OD1 A:ASP520 2.1 39.1 1.0 SG A:CYS524 2.3 24.2 0.5 CG A:ASP520 2.8 40.0 1.0 OD2 A:ASP520 2.9 44.7 1.0 CG A:ASP522 3.1 35.3 1.0 CB A:CYS524 3.2 29.0 0.5 CB A:CYS524 3.2 22.7 0.5 O A:HOH715 3.6 48.6 1.0 OD2 A:ASP522 3.6 39.6 1.0 OD1 A:ASP521 3.9 52.7 1.0 O A:ASP522 4.0 23.4 1.0 N A:CYS524 4.0 20.5 0.5 N A:CYS524 4.0 18.5 0.5 C A:ASP522 4.2 22.8 1.0 CA A:CYS524 4.2 22.9 0.5 CA A:CYS524 4.2 19.4 0.5 N A:ASP522 4.2 30.6 1.0 CB A:ASP520 4.3 36.5 1.0 SG A:CYS524 4.4 35.7 0.5 O A:HOH773 4.4 48.5 1.0 CB A:ASP522 4.4 30.4 1.0 C A:LEU523 4.4 19.6 1.0 O A:LYS518 4.5 23.3 1.0 CE A:LYS518 4.5 45.5 1.0 CA A:ASP522 4.5 26.8 1.0 N A:ASP520 4.5 26.0 1.0 CG A:ASP521 4.6 50.6 1.0 N A:LEU523 4.7 21.3 1.0 CG A:LYS518 4.8 33.3 1.0 N A:ASP521 4.8 39.0 1.0 OD2 A:ASP521 4.9 53.8 1.0 O A:LEU523 4.9 22.2 1.0 CA A:LEU523 4.9 20.7 1.0 CA A:ASP520 4.9 31.9 1.0

Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn binding site number 3 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:Zn601 b:19.7 occ:1.00 OD2 B:ASP529 1.9 19.3 1.0 OE2 B:GLU537 2.0 20.2 1.0 NE2 B:HIS507 2.0 20.0 1.0 O B:HOH711 2.1 20.4 1.0 OE1 B:GLU537 2.4 20.2 1.0 CD B:GLU537 2.5 19.5 1.0 CG B:ASP529 2.8 21.2 1.0 CE1 B:HIS507 3.0 21.5 1.0 OD1 B:ASP529 3.0 19.1 1.0 CD2 B:HIS507 3.1 19.7 1.0 O B:VAL505 3.6 20.9 1.0 O B:HOH739 4.0 23.5 1.0 CG B:GLU537 4.0 20.5 1.0 N B:VAL505 4.1 17.7 1.0 ND1 B:HIS507 4.1 22.0 1.0 CG B:HIS507 4.2 22.3 1.0 CB B:ASP529 4.2 18.4 1.0 CE2 B:PHE538 4.2 19.9 1.0 CZ B:PHE538 4.2 18.9 1.0 CA B:ALA504 4.5 18.1 1.0 C B:VAL505 4.6 20.8 1.0 CB B:ALA504 4.6 18.0 1.0 O B:HOH738 4.6 35.2 1.0 O B:HOH731 4.7 28.2 1.0 C B:ALA504 4.8 17.2 1.0 CG2 B:VAL505 4.8 21.4 1.0 CA B:VAL505 4.9 19.8 1.0 CA B:GLY531 5.0 23.4 1.0

Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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:Zn605 b:26.9 occ:0.89 OD1 B:ASP522 2.0 26.4 1.0 OD1 B:ASP520 2.0 33.1 1.0 OD2 B:ASP520 2.2 34.4 1.0 SG B:CYS524 2.3 25.5 1.0 CG B:ASP520 2.4 27.6 1.0 CG B:ASP522 3.1 26.6 1.0 CB B:CYS524 3.3 24.5 1.0 OD1 B:ASP521 3.5 44.2 1.0 OD2 B:ASP522 3.6 33.1 1.0 CB B:ASP520 3.9 25.2 1.0 NH2 B:ARG571 3.9 33.9 1.0 O B:ASP522 4.0 22.2 1.0 N B:CYS524 4.0 19.8 1.0 N B:ASP522 4.1 28.4 1.0 NH1 B:ARG571 4.1 47.4 1.0 C B:ASP522 4.2 23.2 1.0 CA B:CYS524 4.2 20.6 1.0 CB B:ASP522 4.3 26.6 1.0 CA B:ASP522 4.4 25.2 1.0 C B:LEU523 4.5 19.5 1.0 N B:ASP520 4.5 23.1 1.0 CZ B:ARG571 4.5 42.3 1.0 O B:LYS518 4.5 22.5 1.0 N B:ASP521 4.6 27.9 1.0 CA B:ASP520 4.7 24.2 1.0 CG B:ASP521 4.8 41.4 1.0 N B:LEU523 4.8 20.8 1.0 CB B:LYS518 4.9 26.4 1.0 CE B:LYS518 4.9 41.2 1.0 CA B:LEU523 5.0 20.3 1.0 O B:LEU523 5.0 22.8 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