Copper in PDB 4rkn: Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II

The structure of Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II, PDB code: 4rkn was solved by B.Hermann, M.Kern, L.La Pietra, J.Simon, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.26 / 2.10
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	186.472, 186.472, 232.836, 90.00, 90.00, 120.00
R / Rfree (%)	13.5 / 17.5

The structure of Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II also contains other interesting chemical elements:

Iron

(Fe)

36 atoms

The binding sites of Copper atom in the Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II (pdb code 4rkn). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II, PDB code: 4rkn:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu910 b:15.2 occ:0.40 O3 A:SO3912 1.8 25.9 1.0 SG A:CYS495 2.1 20.4 0.6 SG A:CYS399 2.3 20.3 0.6 CHA A:HEM903 2.8 16.7 1.0 SG A:CYS495 2.9 35.4 0.4 CB A:CYS495 2.9 30.8 0.4 C4D A:HEM903 3.0 18.2 1.0 CB A:CYS495 3.1 22.4 0.6 S A:SO3912 3.1 22.6 1.0 CB A:CYS399 3.2 27.8 0.4 CB A:CYS399 3.2 20.9 0.6 CA A:CYS495 3.3 26.7 0.4 C1A A:HEM903 3.3 19.4 1.0 CA A:CYS495 3.3 21.7 0.6 ND A:HEM903 3.4 17.7 1.0 O A:CYS495 3.5 21.3 0.6 O A:CYS495 3.6 23.9 0.4 SG A:CYS399 3.6 31.6 0.4 O2 A:SO3912 3.7 21.7 1.0 C3D A:HEM903 3.7 18.2 1.0 C A:CYS495 3.8 23.1 0.6 NA A:HEM903 3.8 17.4 1.0 C A:CYS495 3.8 25.8 0.4 NZ A:LYS208 3.9 27.0 1.0 NZ A:LYS393 4.0 24.3 1.0 CE A:LYS208 4.1 24.9 1.0 FE A:HEM903 4.2 19.6 1.0 C2A A:HEM903 4.2 18.9 1.0 CAD A:HEM903 4.2 17.9 1.0 C1D A:HEM903 4.3 17.0 1.0 C2D A:HEM903 4.4 17.0 1.0 O1 A:SO3912 4.5 35.0 1.0 O A:HOH1156 4.5 18.9 1.0 CA A:CYS399 4.6 24.5 0.4 CA A:CYS399 4.6 20.4 0.6 N A:CYS495 4.6 24.7 0.4 N A:CYS495 4.7 21.6 0.6 C4A A:HEM903 4.7 20.9 1.0 CAA A:HEM903 4.8 21.0 1.0 CD A:LYS208 4.9 23.8 1.0 N A:CYS399 5.0 20.9 0.6 N A:CYS399 5.0 23.5 0.4 N A:GLU496 5.0 24.2 1.0

Copper binding site 2 out of 4 in the Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu910 b:11.6 occ:0.40 O2 B:SO3911 1.7 31.3 1.0 SG B:CYS495 2.1 21.0 0.6 SG B:CYS399 2.2 20.6 0.6 SG B:CYS495 2.7 28.8 0.4 CHA B:HEM903 2.8 17.2 1.0 CB B:CYS495 2.9 26.2 0.4 C4D B:HEM903 3.1 17.1 1.0 CB B:CYS495 3.1 21.5 0.6 CB B:CYS399 3.1 19.9 0.6 S B:SO3911 3.2 23.7 1.0 CB B:CYS399 3.2 24.6 0.4 CA B:CYS495 3.3 25.6 0.4 C1A B:HEM903 3.3 20.1 1.0 CA B:CYS495 3.3 22.8 0.6 ND B:HEM903 3.5 15.8 1.0 SG B:CYS399 3.5 27.8 0.4 O B:CYS495 3.5 21.4 0.6 O B:CYS495 3.6 23.2 0.4 O1 B:SO3911 3.6 23.0 1.0 NA B:HEM903 3.8 18.3 1.0 C3D B:HEM903 3.8 16.5 1.0 C B:CYS495 3.8 21.8 0.6 C B:CYS495 3.8 23.5 0.4 NZ B:LYS393 3.9 23.1 1.0 CE B:LYS208 4.1 22.5 1.0 NZ B:LYS208 4.1 27.9 1.0 FE B:HEM903 4.2 18.8 1.0 C2A B:HEM903 4.2 18.8 1.0 CAD B:HEM903 4.2 17.8 1.0 C1D B:HEM903 4.3 16.5 1.0 O3 B:SO3911 4.4 34.9 1.0 C2D B:HEM903 4.5 16.7 1.0 O B:HOH1115 4.5 20.7 1.0 CA B:CYS399 4.5 20.0 0.6 CA B:CYS399 4.6 22.8 0.4 N B:CYS495 4.6 24.2 0.4 N B:CYS495 4.7 22.3 0.6 C4A B:HEM903 4.7 20.4 1.0 CAA B:HEM903 4.8 18.7 1.0 CD B:LYS208 4.9 20.8 1.0 N B:CYS399 5.0 23.6 0.4 N B:CYS399 5.0 22.1 0.6

Copper binding site 3 out of 4 in the Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu910 b:17.7 occ:0.40 O2 C:SO3911 1.6 30.4 1.0 SG C:CYS399 2.1 23.2 0.6 SG C:CYS495 2.2 25.6 0.6 SG C:CYS495 2.8 36.6 0.4 CHA C:HEM903 2.9 20.6 1.0 CB C:CYS495 2.9 30.4 0.4 CB C:CYS399 3.0 24.0 0.6 CB C:CYS495 3.1 24.0 0.6 CB C:CYS399 3.1 29.3 0.4 C4D C:HEM903 3.1 20.3 1.0 S C:SO3911 3.2 25.5 1.0 CA C:CYS495 3.3 29.2 0.4 CA C:CYS495 3.3 25.5 0.6 C1A C:HEM903 3.4 20.4 1.0 O C:CYS495 3.4 22.2 0.6 O C:CYS495 3.5 25.6 0.4 SG C:CYS399 3.6 31.1 0.4 ND C:HEM903 3.6 20.0 1.0 O1 C:SO3911 3.7 23.1 1.0 C C:CYS495 3.7 27.0 0.6 C C:CYS495 3.8 29.1 0.4 C3D C:HEM903 3.8 20.5 1.0 NZ C:LYS393 3.8 28.1 1.0 NA C:HEM903 3.9 19.5 1.0 NZ C:LYS208 3.9 27.2 1.0 CE C:LYS208 4.3 26.1 1.0 FE C:HEM903 4.3 21.4 1.0 CAD C:HEM903 4.3 20.7 1.0 C2A C:HEM903 4.3 21.1 1.0 C1D C:HEM903 4.3 19.5 1.0 O3 C:SO3911 4.4 38.2 1.0 O C:HOH1110 4.4 20.0 1.0 CA C:CYS399 4.5 24.7 0.6 C2D C:HEM903 4.5 19.4 1.0 CA C:CYS399 4.5 27.8 0.4 N C:CYS495 4.6 24.8 0.4 N C:CYS495 4.6 21.7 0.6 C4A C:HEM903 4.8 21.3 1.0 CAA C:HEM903 4.9 20.1 1.0 N C:GLU496 5.0 28.5 1.0 N C:CYS399 5.0 26.9 0.4 N C:CYS399 5.0 24.7 0.6

Copper binding site 4 out of 4 in the Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Wolinella Succinogenes Octaheme Sulfite Reductase Mcca, Form II within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu910 b:9.5 occ:0.40 O3 D:SO3912 1.3 21.4 1.0 SG D:CYS495 2.2 15.5 0.5 SG D:CYS399 2.2 13.5 0.6 CB D:CYS495 2.7 26.3 0.5 SG D:CYS495 2.8 37.0 0.5 CHA D:HEM903 2.8 13.5 1.0 CB D:CYS399 3.0 21.3 0.4 C4D D:HEM903 3.1 13.2 1.0 CB D:CYS399 3.1 14.2 0.6 S D:SO3912 3.1 17.5 1.0 CB D:CYS495 3.1 16.1 0.5 CA D:CYS495 3.2 22.9 0.5 CA D:CYS495 3.3 17.4 0.5 C1A D:HEM903 3.3 13.0 1.0 SG D:CYS399 3.3 24.4 0.4 O D:CYS495 3.5 20.5 0.5 ND D:HEM903 3.5 12.0 1.0 O D:CYS495 3.6 23.6 0.5 C3D D:HEM903 3.7 12.8 1.0 O2 D:SO3912 3.8 15.6 1.0 C D:CYS495 3.8 18.0 0.5 NA D:HEM903 3.8 11.7 1.0 C D:CYS495 3.9 20.9 0.5 NZ D:LYS393 3.9 20.5 1.0 CAD D:HEM903 4.2 13.6 1.0 CE D:LYS208 4.2 18.5 1.0 NZ D:LYS208 4.3 21.1 1.0 FE D:HEM903 4.3 13.3 1.0 C1D D:HEM903 4.3 12.9 1.0 C2A D:HEM903 4.3 13.3 1.0 C2D D:HEM903 4.4 13.1 1.0 O D:HOH1091 4.4 16.7 1.0 CA D:CYS399 4.5 19.3 0.4 CA D:CYS399 4.5 15.1 0.6 N D:CYS495 4.5 20.2 0.5 O1 D:SO3912 4.5 24.2 1.0 N D:CYS495 4.7 17.3 0.5 C4A D:HEM903 4.8 12.9 1.0 CAA D:HEM903 4.8 13.4 1.0 N D:CYS399 4.9 19.3 0.4 N D:CYS399 4.9 16.8 0.6 CE D:LYS393 4.9 20.6 1.0

B.Hermann, M.Kern, L.La Pietra, J.Simon, O.Einsle. The Octahaem Mcca Is A Haem C-Copper Sulphite Reductase Nature 2015.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE14109