Iron 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
Copper	(Cu)	2 atoms

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 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 Iron with other atoms in the Fe 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:Fe1001 b:1.0 occ:1.00 FE A:HEA1001 0.0 1.0 1.0 NA A:HEA1001 2.0 0.7 1.0 NC A:HEA1001 2.1 0.6 1.0 NB A:HEA1001 2.1 0.5 1.0 ND A:HEA1001 2.1 0.6 1.0 NE2 A:HIS102 2.3 0.4 1.0 NE2 A:HIS417 2.8 88.8 1.0 C1A A:HEA1001 2.9 0.2 1.0 C4A A:HEA1001 2.9 0.0 1.0 CD2 A:HIS102 2.9 0.6 1.0 C1C A:HEA1001 3.1 0.7 1.0 C4B A:HEA1001 3.1 0.4 1.0 C4C A:HEA1001 3.1 0.5 1.0 C4D A:HEA1001 3.1 1.0 1.0 C1B A:HEA1001 3.1 0.8 1.0 C1D A:HEA1001 3.1 0.6 1.0 CHA A:HEA1001 3.3 0.3 1.0 CHC A:HEA1001 3.4 0.3 1.0 CHB A:HEA1001 3.4 0.7 1.0 CHD A:HEA1001 3.5 0.8 1.0 CE1 A:HIS102 3.5 0.5 1.0 CD2 A:HIS417 3.7 98.2 1.0 CE1 A:HIS417 3.8 98.0 1.0 C3A A:HEA1001 4.0 0.0 1.0 C2A A:HEA1001 4.1 0.0 1.0 CG A:HIS102 4.2 0.8 1.0 C3C A:HEA1001 4.4 0.8 1.0 C2B A:HEA1001 4.4 0.4 1.0 C3B A:HEA1001 4.4 1.0 1.0 C2C A:HEA1001 4.4 0.0 1.0 C2D A:HEA1001 4.4 0.9 1.0 C3D A:HEA1001 4.4 0.9 1.0 ND1 A:HIS102 4.5 0.1 1.0 CG A:HIS417 4.9 0.1 1.0 ND1 A:HIS417 4.9 0.4 1.0

Iron binding site 2 out of 4 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 Iron with other atoms in the Fe 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 A:Fe1002 b:0.3 occ:1.00 FE A:HEA1002 0.0 0.3 1.0 NA A:HEA1002 2.0 0.6 1.0 NC A:HEA1002 2.1 0.6 1.0 NB A:HEA1002 2.1 0.0 1.0 ND A:HEA1002 2.1 0.6 1.0 C1A A:HEA1002 3.0 0.3 1.0 C4A A:HEA1002 3.0 0.1 1.0 NE2 A:HIS415 3.1 71.0 1.0 C4D A:HEA1002 3.1 0.1 1.0 C4C A:HEA1002 3.1 0.8 1.0 C4B A:HEA1002 3.1 0.3 1.0 C1C A:HEA1002 3.1 0.7 1.0 C1B A:HEA1002 3.1 0.0 1.0 C1D A:HEA1002 3.2 0.6 1.0 CHA A:HEA1002 3.4 0.1 1.0 CHB A:HEA1002 3.5 0.3 1.0 CHC A:HEA1002 3.5 0.5 1.0 CHD A:HEA1002 3.5 0.1 1.0 CE1 A:HIS415 3.8 91.2 1.0 CD2 A:HIS415 4.1 82.2 1.0 C3A A:HEA1002 4.1 0.0 1.0 C2A A:HEA1002 4.2 0.7 1.0 C3C A:HEA1002 4.4 0.9 1.0 C3B A:HEA1002 4.5 0.4 1.0 C2B A:HEA1002 4.5 0.7 1.0 NE2 A:HIS329 4.5 0.4 1.0 C3D A:HEA1002 4.5 0.3 1.0 C2C A:HEA1002 4.5 0.7 1.0 C2D A:HEA1002 4.5 0.2 1.0 CE1 A:HIS329 4.8 0.3 1.0 CE1 A:HIS280 4.9 0.1 1.0

Iron binding site 3 out of 4 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 Iron with other atoms in the Fe binding site number 3 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:Fe1001 b:0.4 occ:1.00 FE E:HEA1001 0.0 0.4 1.0 NA E:HEA1001 2.0 0.9 1.0 NC E:HEA1001 2.1 0.9 1.0 NB E:HEA1001 2.1 0.3 1.0 ND E:HEA1001 2.1 0.4 1.0 NE2 E:HIS102 2.3 0.1 1.0 NE2 E:HIS417 2.7 87.4 1.0 C1A E:HEA1001 2.9 0.4 1.0 C4A E:HEA1001 2.9 0.7 1.0 CD2 E:HIS102 3.0 0.9 1.0 C4B E:HEA1001 3.1 0.9 1.0 C1C E:HEA1001 3.1 0.8 1.0 C1B E:HEA1001 3.1 0.6 1.0 C4C E:HEA1001 3.1 0.2 1.0 C4D E:HEA1001 3.1 0.7 1.0 C1D E:HEA1001 3.1 99.0 1.0 CHA E:HEA1001 3.3 0.7 1.0 CHC E:HEA1001 3.4 0.6 1.0 CHB E:HEA1001 3.4 0.6 1.0 CHD E:HEA1001 3.4 0.1 1.0 CE1 E:HIS102 3.5 0.2 1.0 CE1 E:HIS417 3.7 92.2 1.0 CD2 E:HIS417 3.7 94.7 1.0 C3A E:HEA1001 4.0 0.3 1.0 C2A E:HEA1001 4.1 0.3 1.0 CG E:HIS102 4.2 0.8 1.0 ND1 E:HIS102 4.4 0.2 1.0 C3C E:HEA1001 4.4 0.9 1.0 C2B E:HEA1001 4.4 0.8 1.0 C3B E:HEA1001 4.4 0.8 1.0 C2D E:HEA1001 4.4 88.6 1.0 C2C E:HEA1001 4.4 0.9 1.0 C3D E:HEA1001 4.4 0.5 1.0 ND1 E:HIS417 4.8 0.9 1.0 CG E:HIS417 4.9 0.1 1.0

Iron binding site 4 out of 4 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 Iron with other atoms in the Fe binding site number 4 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:Fe1002 b:0.0 occ:1.00 FE E:HEA1002 0.0 0.0 1.0 NA E:HEA1002 2.0 0.1 1.0 NC E:HEA1002 2.1 0.2 1.0 NB E:HEA1002 2.1 0.3 1.0 ND E:HEA1002 2.1 0.7 1.0 C1A E:HEA1002 3.0 0.9 1.0 C4A E:HEA1002 3.0 0.9 1.0 NE2 E:HIS415 3.0 92.6 1.0 C4C E:HEA1002 3.1 0.7 1.0 C1C E:HEA1002 3.1 0.7 1.0 C4D E:HEA1002 3.1 0.5 1.0 C1B E:HEA1002 3.1 0.9 1.0 C4B E:HEA1002 3.1 0.3 1.0 C1D E:HEA1002 3.2 0.8 1.0 CHA E:HEA1002 3.4 0.4 1.0 CHB E:HEA1002 3.5 0.8 1.0 CHC E:HEA1002 3.5 1.0 1.0 CHD E:HEA1002 3.5 0.2 1.0 CE1 E:HIS415 3.8 96.3 1.0 CD2 E:HIS415 4.0 92.0 1.0 C3A E:HEA1002 4.1 0.6 1.0 C2A E:HEA1002 4.1 0.1 1.0 CU E:CU1003 4.4 0.5 1.0 C3C E:HEA1002 4.4 0.8 1.0 C3B E:HEA1002 4.5 0.2 1.0 C2C E:HEA1002 4.5 0.6 1.0 C2B E:HEA1002 4.5 0.0 1.0 C3D E:HEA1002 4.5 0.2 1.0 C2D E:HEA1002 4.5 0.9 1.0 CE1 E:HIS280 4.9 0.3 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