Copper 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:

Zinc

(Zn)

2 atoms

The binding sites of Copper 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 Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of Cu/Zn Superoxide Dismutase From Paenibacillus Lautus, PDB code: 8imd:
Jump to Copper binding site number: 1; 2;

Copper 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 Copper with other atoms in the Cu 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:Cu302 b:19.0 occ:1.00 NE2 A:HIS121 2.0 14.5 1.0 ND1 A:HIS119 2.0 14.8 1.0 NE2 A:HIS195 2.0 14.4 1.0 NE2 A:HIS136 2.9 18.0 1.0 CE1 A:HIS121 2.9 16.2 1.0 CE1 A:HIS119 3.0 14.7 1.0 CD2 A:HIS195 3.0 15.6 1.0 CD2 A:HIS121 3.0 15.2 1.0 CG A:HIS119 3.0 15.0 1.0 CE1 A:HIS195 3.1 16.6 1.0 CB A:HIS119 3.4 13.7 1.0 CD2 A:HIS136 3.4 17.1 1.0 O A:HOH541 3.7 27.8 1.0 CE1 A:HIS136 3.7 16.6 1.0 ND1 A:HIS121 4.0 15.4 1.0 NE2 A:HIS119 4.1 14.5 1.0 CB A:ILE193 4.1 14.5 1.0 CG A:HIS121 4.1 14.1 1.0 CG A:HIS195 4.1 15.0 1.0 CD2 A:HIS119 4.1 15.0 1.0 ND1 A:HIS195 4.2 17.0 1.0 CG2 A:ILE193 4.2 15.0 1.0 N A:HIS119 4.2 14.2 1.0 CA A:HIS119 4.3 14.8 1.0 O A:ILE193 4.4 13.5 1.0 CG A:HIS136 4.5 15.4 1.0 ND1 A:HIS136 4.6 15.4 1.0 O A:HIS119 4.6 14.1 1.0 C A:HIS119 4.8 14.1 1.0 CG1 A:ILE193 4.9 15.9 1.0 C A:ILE193 4.9 12.6 1.0

Copper 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 Copper with other atoms in the Cu 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:Cu302 b:22.2 occ:1.00 NE2 B:HIS121 2.0 18.0 1.0 ND1 B:HIS119 2.0 17.4 1.0 NE2 B:HIS195 2.0 21.3 1.0 CE1 B:HIS119 2.9 20.2 1.0 CE1 B:HIS121 3.0 18.4 1.0 CD2 B:HIS195 3.0 18.8 1.0 CG B:HIS119 3.0 17.8 1.0 NE2 B:HIS136 3.0 20.7 1.0 CD2 B:HIS121 3.1 15.9 1.0 CE1 B:HIS195 3.1 22.2 1.0 CB B:HIS119 3.4 16.8 1.0 O B:HOH490 3.5 27.9 1.0 CD2 B:HIS136 3.6 18.9 1.0 CE1 B:HIS136 3.9 18.9 1.0 CB B:ILE193 4.0 18.5 1.0 NE2 B:HIS119 4.1 19.2 1.0 ND1 B:HIS121 4.1 18.8 1.0 CD2 B:HIS119 4.1 19.9 1.0 CG2 B:ILE193 4.1 20.1 1.0 CG B:HIS195 4.1 19.9 1.0 CG B:HIS121 4.1 16.7 1.0 ND1 B:HIS195 4.2 21.4 1.0 N B:HIS119 4.2 15.3 1.0 CA B:HIS119 4.3 14.8 1.0 O B:ILE193 4.3 17.5 1.0 CG B:HIS136 4.6 16.4 1.0 O B:HIS119 4.7 15.4 1.0 C B:HIS119 4.8 15.1 1.0 ND1 B:HIS136 4.8 18.6 1.0 C B:ILE193 4.8 16.1 1.0 CG1 B:ILE193 4.9 19.9 1.0 CA B:ILE193 5.0 17.3 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