Copper in PDB 6koc: X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis Complexed with 3-Iodo-N-Oxo-2-Heptyl- 4-Hydroxyquinoline

The structure of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis Complexed with 3-Iodo-N-Oxo-2-Heptyl- 4-Hydroxyquinoline, PDB code: 6koc 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)	48.27 / 3.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	113.930, 162.200, 151.320, 90.00, 109.76, 90.00
R / Rfree (%)	32.5 / 36.9

The structure of X-Ray Structure of the Proton-Pumping Cytochrome AA3-600 Menaquinol Oxidase From Bacillus Subtilis Complexed with 3-Iodo-N-Oxo-2-Heptyl- 4-Hydroxyquinoline also contains other interesting chemical elements:

Iodine	(I)	2 atoms
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 Complexed with 3-Iodo-N-Oxo-2-Heptyl- 4-Hydroxyquinoline (pdb code 6koc). 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 Complexed with 3-Iodo-N-Oxo-2-Heptyl- 4-Hydroxyquinoline, PDB code: 6koc:
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 Complexed with 3-Iodo-N-Oxo-2-Heptyl- 4-Hydroxyquinoline


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 Complexed with 3-Iodo-N-Oxo-2-Heptyl- 4-Hydroxyquinoline within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1003 b:0.2 occ:1.00 ND1 A:HIS280 2.1 0.3 1.0 NE2 A:HIS329 2.3 0.4 1.0 NE2 A:HIS330 2.3 0.6 1.0 CE1 A:HIS329 2.4 0.3 1.0 CG A:HIS280 2.5 0.0 1.0 CD2 A:HIS330 2.8 0.1 1.0 CD2 A:HIS329 2.9 0.4 1.0 CE1 A:HIS280 2.9 0.1 1.0 ND1 A:HIS329 3.0 0.3 1.0 CB A:HIS280 3.0 71.3 1.0 CG A:HIS329 3.3 0.8 1.0 CE1 A:HIS330 3.3 0.9 1.0 CD2 A:HIS280 3.4 0.4 1.0 NE2 A:HIS280 3.6 0.5 1.0 CG A:HIS330 4.0 0.1 1.0 O A:VAL326 4.1 98.3 1.0 ND1 A:HIS330 4.2 0.5 1.0 CA A:HIS280 4.2 63.3 1.0 CA A:TRP327 4.2 0.7 1.0 O A:TRP327 4.5 90.6 1.0 CB A:HIS329 4.5 0.9 1.0 C A:TRP327 4.6 0.4 1.0 C A:VAL326 4.7 1.0 1.0 N A:TRP327 4.8 0.1 1.0 N A:HIS330 4.9 90.3 1.0 N A:HIS280 5.0 57.0 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 Complexed with 3-Iodo-N-Oxo-2-Heptyl- 4-Hydroxyquinoline


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 Complexed with 3-Iodo-N-Oxo-2-Heptyl- 4-Hydroxyquinoline within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu1003 b:0.5 occ:1.00 ND1 E:HIS280 2.0 1.0 1.0 NE2 E:HIS329 2.0 0.2 1.0 NE2 E:HIS330 2.1 0.7 1.0 CE1 E:HIS330 2.7 0.4 1.0 CE1 E:HIS329 2.7 87.3 1.0 CE1 E:HIS280 2.9 0.3 1.0 CG E:HIS280 3.0 0.8 1.0 CD2 E:HIS329 3.2 98.7 1.0 CD2 E:HIS330 3.2 0.7 1.0 CB E:HIS280 3.4 85.4 1.0 ND1 E:HIS330 3.8 0.4 1.0 NE2 E:HIS280 3.9 0.7 1.0 ND1 E:HIS329 3.9 99.7 1.0 CD2 E:HIS280 4.0 0.5 1.0 CG E:HIS330 4.1 0.0 1.0 CA E:HIS280 4.1 80.5 1.0 CG E:HIS329 4.2 0.8 1.0 FE E:HEA1002 4.4 0.0 1.0 ND E:HEA1002 4.4 0.7 1.0 C1A E:HEA1002 4.7 0.9 1.0 CG1 E:VAL283 4.7 58.5 1.0 C2A E:HEA1002 4.7 0.1 1.0 C1D E:HEA1002 4.8 0.8 1.0 C4D E:HEA1002 4.9 0.5 1.0 NA E:HEA1002 4.9 0.1 1.0 C3A E:HEA1002 4.9 0.6 1.0 N E:HIS280 4.9 88.1 1.0 C4A E:HEA1002 4.9 0.9 1.0 NC E:HEA1002 5.0 0.2 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