Copper in PDB 6koe: X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis

The structure of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis, PDB code: 6koe was solved by J.Xu, Z.Ding, B.Liu, J.Li, R.B.Gennis, J.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.25 / 3.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	112.988, 162.110, 149.509, 90.00, 109.02, 90.00
R / Rfree (%)	34.7 / 36.8

The structure of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Copper atom in the X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis (pdb code 6koe). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis, PDB code: 6koe:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1003 b:0.7 occ:1.00 CE1 A:HIS329 2.0 0.7 1.0 ND1 A:HIS280 2.0 0.1 1.0 NE2 A:HIS329 2.1 0.0 1.0 NE2 A:HIS330 2.1 0.8 1.0 CG A:HIS280 2.7 0.7 1.0 CE1 A:HIS330 2.9 0.3 1.0 CE1 A:HIS280 2.9 0.8 1.0 CB A:HIS280 3.1 95.2 1.0 CD2 A:HIS330 3.1 0.3 1.0 ND1 A:HIS329 3.3 0.4 1.0 CD2 A:HIS329 3.4 0.5 1.0 CD2 A:HIS280 3.7 0.9 1.0 NE2 A:HIS280 3.8 0.3 1.0 CG A:HIS329 3.9 0.2 1.0 ND1 A:HIS330 3.9 0.7 1.0 CA A:HIS280 4.0 94.2 1.0 CG A:HIS330 4.1 0.8 1.0 N A:HIS280 4.8 91.1 1.0 FE A:HEA1002 4.9 0.3 1.0 C2A A:HEA1002 4.9 0.3 1.0 C1A A:HEA1002 4.9 0.4 1.0 ND A:HEA1002 4.9 0.7 1.0 C3A A:HEA1002 5.0 0.8 1.0

Copper binding site 2 out of 2 in the X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu1003 b:0.5 occ:1.00 NE2 E:HIS329 2.0 99.4 1.0 ND1 E:HIS280 2.0 99.2 1.0 NE2 E:HIS330 2.1 0.1 1.0 CE1 E:HIS330 2.6 0.9 1.0 CE1 E:HIS329 2.6 96.7 1.0 CG E:HIS280 2.9 91.7 1.0 CE1 E:HIS280 2.9 0.9 1.0 CD2 E:HIS330 3.2 97.6 1.0 CB E:HIS280 3.3 83.0 1.0 CD2 E:HIS329 3.3 98.4 1.0 ND1 E:HIS330 3.7 0.2 1.0 ND1 E:HIS329 3.9 95.2 1.0 NE2 E:HIS280 3.9 0.1 1.0 CD2 E:HIS280 3.9 94.0 1.0 CA E:HIS280 4.0 79.9 1.0 CG E:HIS330 4.1 97.6 1.0 CG E:HIS329 4.2 96.7 1.0 FE E:HEA1002 4.4 0.4 1.0 ND E:HEA1002 4.5 0.9 1.0 CG1 E:VAL283 4.6 89.1 1.0 C1A E:HEA1002 4.7 0.6 1.0 C2A E:HEA1002 4.7 0.9 1.0 CG2 E:VAL283 4.8 89.6 1.0 CB E:VAL283 4.9 84.8 1.0 N E:HIS280 4.9 77.1 1.0 C4D E:HEA1002 4.9 0.8 1.0 C3A E:HEA1002 4.9 0.9 1.0 NA E:HEA1002 4.9 0.7 1.0 C1D E:HEA1002 4.9 0.4 1.0 C4A E:HEA1002 4.9 0.2 1.0 NC E:HEA1002 5.0 0.8 1.0

J.Xu, Z.Ding, B.Liu, S.M.Yi, J.Li, Z.Zhang, Y.Liu, J.Li, L.Liu, A.Zhou, R.B.Gennis, J.Zhu. Structure of the Cytochrome AA3-600 Heme-Copper Menaquinol Oxidase Bound to Inhibitor Hqno Shows TM0 Is Part of the Quinol Binding Site Proc.Natl.Acad.Sci.Usa 2010.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1915013117