Zinc in PDB 8imd: Crystal Structure of Cu/Zn Superoxide Dismutase From Paenibacillus Lautus

The structure of Crystal Structure of Cu/Zn Superoxide Dismutase From Paenibacillus Lautus, PDB code: 8imd was solved by S.Narikiyo, Y.Furukawa, M.Akutsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.35 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.24, 53.612, 169.567, 90, 90, 90
R / Rfree (%)	18.8 / 22.1

The structure of Crystal Structure of Cu/Zn Superoxide Dismutase From Paenibacillus Lautus also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Cu/Zn Superoxide Dismutase From Paenibacillus Lautus (pdb code 8imd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Cu/Zn Superoxide Dismutase From Paenibacillus Lautus, PDB code: 8imd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Cu/Zn Superoxide Dismutase From Paenibacillus Lautus


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 Cu/Zn Superoxide Dismutase From Paenibacillus Lautus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:16.2 occ:1.00 ND1 A:HIS136 2.0 15.4 1.0 OD1 A:ASP156 2.0 17.2 1.0 ND1 A:HIS153 2.0 16.5 1.0 ND1 A:HIS144 2.1 14.6 1.0 CE1 A:HIS144 2.8 16.6 1.0 CG A:ASP156 2.8 15.4 1.0 CE1 A:HIS153 2.8 16.3 1.0 CE1 A:HIS136 3.0 16.6 1.0 CG A:HIS136 3.0 15.4 1.0 OD2 A:ASP156 3.0 17.2 1.0 CG A:HIS153 3.1 17.2 1.0 CG A:HIS144 3.2 16.2 1.0 CB A:HIS136 3.4 16.1 1.0 CB A:HIS153 3.5 17.9 1.0 CB A:HIS144 3.7 18.4 1.0 O A:PRO205 3.8 19.9 1.0 CA A:HIS144 4.0 19.1 1.0 NE2 A:HIS153 4.0 20.4 1.0 NE2 A:HIS144 4.1 17.3 1.0 NE2 A:HIS136 4.1 18.0 1.0 CD2 A:HIS136 4.1 17.1 1.0 CD2 A:HIS153 4.1 18.1 1.0 CD2 A:HIS144 4.2 16.1 1.0 CB A:ASP156 4.3 15.5 1.0 CD2 A:HIS119 4.6 15.0 1.0 N A:GLY145 4.6 19.7 1.0 CA A:ASP156 4.7 16.1 1.0 O A:HOH508 4.8 22.9 1.0 CA A:HIS153 4.8 19.4 1.0 C A:HIS144 4.8 21.0 1.0 CG A:HIS119 4.9 15.0 1.0 C A:PRO205 4.9 23.4 1.0 N A:ASP156 4.9 16.4 1.0 N A:HIS153 4.9 19.6 1.0 CA A:SER206 4.9 19.2 1.0 CA A:HIS136 4.9 16.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Cu/Zn Superoxide Dismutase From Paenibacillus Lautus


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 Cu/Zn Superoxide Dismutase From Paenibacillus Lautus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:19.8 occ:1.00 OD1 B:ASP156 2.0 15.6 1.0 ND1 B:HIS136 2.0 18.6 1.0 ND1 B:HIS153 2.0 22.2 1.0 ND1 B:HIS144 2.1 20.1 1.0 CG B:ASP156 2.8 20.9 1.0 CE1 B:HIS144 2.9 20.0 1.0 CE1 B:HIS136 2.9 18.9 1.0 CE1 B:HIS153 2.9 22.4 1.0 OD2 B:ASP156 3.0 19.8 1.0 CG B:HIS136 3.0 16.4 1.0 CG B:HIS153 3.1 18.8 1.0 CG B:HIS144 3.2 21.6 1.0 CB B:HIS136 3.4 18.0 1.0 CB B:HIS153 3.5 19.6 1.0 CB B:HIS144 3.7 22.6 1.0 O B:PRO205 3.8 29.3 1.0 CA B:HIS144 4.0 23.1 1.0 NE2 B:HIS136 4.1 20.7 1.0 NE2 B:HIS153 4.1 22.5 1.0 NE2 B:HIS144 4.1 22.1 1.0 CD2 B:HIS136 4.1 18.9 1.0 CD2 B:HIS153 4.2 22.9 1.0 CB B:ASP156 4.2 19.7 1.0 CD2 B:HIS144 4.2 21.1 1.0 CD2 B:HIS119 4.6 19.9 1.0 N B:GLY145 4.6 24.2 1.0 CA B:ASP156 4.7 17.2 1.0 CA B:HIS153 4.8 21.5 1.0 N B:HIS153 4.8 19.9 1.0 C B:PRO205 4.9 33.7 1.0 C B:HIS144 4.9 26.0 1.0 CA B:HIS136 4.9 17.8 1.0 N B:ASP156 4.9 16.4 1.0 CG B:HIS119 4.9 17.8 1.0 CA B:SER206 4.9 34.1 1.0 O B:HOH482 4.9 24.9 1.0

Y.Furukawa, A.Shintani, S.Narikiyo, K.Sue, M.Akutsu, N.Muraki. Characterization of A Novel Cysteine-Less Cu/Zn-Superoxide Dismutase in Paenibacillus Lautus Missing A Conserved Disulfide Bond. J.Biol.Chem. V. 299 05040 2023.
ISSN: ESSN 1083-351X
PubMed: 37442237
DOI: 10.1016/J.JBC.2023.105040