Iron in PDB 6nmf: Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

The structure of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature, PDB code: 6nmf was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	178.700, 189.800, 211.300, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.2

The structure of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	2 atoms
Copper	(Cu)	6 atoms
Sodium	(Na)	2 atoms

The binding sites of Iron atom in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature (pdb code 6nmf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature, PDB code: 6nmf:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:44.9 occ:1.00 FE A:HEA601 0.0 44.9 1.0 NE2 A:HIS378 2.0 44.4 1.0 ND A:HEA601 2.1 42.7 1.0 NE2 A:HIS61 2.1 45.2 1.0 NA A:HEA601 2.1 47.8 1.0 NB A:HEA601 2.1 47.8 1.0 NC A:HEA601 2.1 48.8 1.0 CE1 A:HIS378 2.9 48.4 1.0 CD2 A:HIS61 3.1 46.8 1.0 C4A A:HEA601 3.1 48.1 1.0 CE1 A:HIS61 3.1 43.1 1.0 C4D A:HEA601 3.1 42.2 1.0 C1D A:HEA601 3.1 42.9 1.0 CD2 A:HIS378 3.1 45.3 1.0 C1A A:HEA601 3.1 46.2 1.0 C1B A:HEA601 3.1 49.2 1.0 C4C A:HEA601 3.1 44.4 1.0 C4B A:HEA601 3.1 47.6 1.0 C1C A:HEA601 3.1 46.9 1.0 CHB A:HEA601 3.4 47.9 1.0 CHA A:HEA601 3.5 42.5 1.0 CHD A:HEA601 3.5 42.1 1.0 CHC A:HEA601 3.5 45.4 1.0 ND1 A:HIS378 4.1 48.7 1.0 ND1 A:HIS61 4.2 43.3 1.0 CG A:HIS378 4.2 44.9 1.0 CG A:HIS61 4.2 44.9 1.0 C3A A:HEA601 4.4 49.4 1.0 C3D A:HEA601 4.4 43.8 1.0 C2D A:HEA601 4.4 42.8 1.0 C2A A:HEA601 4.4 47.3 1.0 C3C A:HEA601 4.4 43.2 1.0 C2B A:HEA601 4.4 50.4 1.0 C2C A:HEA601 4.5 44.0 1.0 C3B A:HEA601 4.5 49.0 1.0

Iron binding site 2 out of 4 in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:44.6 occ:1.00 FE A:HEA602 0.0 44.6 1.0 NB A:HEA602 2.1 42.9 1.0 ND A:HEA602 2.1 43.2 1.0 NA A:HEA602 2.1 43.1 1.0 NC A:HEA602 2.1 43.3 1.0 NE2 A:HIS376 2.1 47.0 1.0 CD2 A:HIS376 3.1 49.8 1.0 CE1 A:HIS376 3.1 47.8 1.0 C4D A:HEA602 3.1 43.5 1.0 C4A A:HEA602 3.1 43.5 1.0 C4B A:HEA602 3.1 43.9 1.0 C1B A:HEA602 3.1 42.3 1.0 C1C A:HEA602 3.1 42.9 1.0 C1A A:HEA602 3.1 41.6 1.0 C1D A:HEA602 3.1 41.8 1.0 C4C A:HEA602 3.1 41.9 1.0 CHA A:HEA602 3.5 43.2 1.0 CHB A:HEA602 3.5 44.8 1.0 CHC A:HEA602 3.5 42.0 1.0 CHD A:HEA602 3.5 42.0 1.0 ND1 A:HIS376 4.2 45.2 1.0 CG A:HIS376 4.2 47.5 1.0 C3A A:HEA602 4.4 41.5 1.0 C3B A:HEA602 4.4 46.4 1.0 C3D A:HEA602 4.4 43.6 1.0 C2B A:HEA602 4.4 42.8 1.0 C3C A:HEA602 4.4 44.4 1.0 C2D A:HEA602 4.4 41.4 1.0 C2C A:HEA602 4.4 42.7 1.0 C2A A:HEA602 4.4 40.6 1.0

Iron binding site 3 out of 4 in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe601 b:59.5 occ:1.00 FE N:HEA601 0.0 59.5 1.0 NE2 N:HIS61 2.1 67.1 1.0 NE2 N:HIS378 2.1 60.6 1.0 NC N:HEA601 2.1 56.4 1.0 NA N:HEA601 2.1 56.2 1.0 ND N:HEA601 2.1 60.9 1.0 NB N:HEA601 2.1 58.9 1.0 CD2 N:HIS61 2.9 66.1 1.0 CE1 N:HIS378 3.0 61.1 1.0 C4A N:HEA601 3.1 56.4 1.0 C1C N:HEA601 3.1 60.0 1.0 C4C N:HEA601 3.1 59.4 1.0 C1B N:HEA601 3.1 57.1 1.0 C1D N:HEA601 3.1 62.7 1.0 C4D N:HEA601 3.1 59.5 1.0 C4B N:HEA601 3.1 57.6 1.0 C1A N:HEA601 3.1 62.0 1.0 CD2 N:HIS378 3.1 62.9 1.0 CE1 N:HIS61 3.2 70.2 1.0 CHB N:HEA601 3.4 53.4 1.0 CHC N:HEA601 3.5 58.3 1.0 CHD N:HEA601 3.5 59.0 1.0 CHA N:HEA601 3.5 61.2 1.0 CG N:HIS61 4.1 68.8 1.0 ND1 N:HIS378 4.1 61.6 1.0 ND1 N:HIS61 4.2 68.1 1.0 CG N:HIS378 4.2 65.8 1.0 C3A N:HEA601 4.4 63.5 1.0 C3C N:HEA601 4.4 61.2 1.0 C3D N:HEA601 4.4 61.2 1.0 C2B N:HEA601 4.4 62.9 1.0 C2D N:HEA601 4.4 61.9 1.0 C2C N:HEA601 4.4 64.3 1.0 C3B N:HEA601 4.4 59.1 1.0 C2A N:HEA601 4.5 63.0 1.0 OG N:SER382 4.8 0.1 1.0

Iron binding site 4 out of 4 in the Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe602 b:52.8 occ:1.00 FE N:HEA602 0.0 52.8 1.0 NA N:HEA602 2.1 48.0 1.0 NB N:HEA602 2.1 47.9 1.0 NC N:HEA602 2.1 46.0 1.0 ND N:HEA602 2.1 51.6 1.0 NE2 N:HIS376 2.1 66.3 1.0 CE1 N:HIS376 3.0 73.0 1.0 C1B N:HEA602 3.1 51.7 1.0 C1A N:HEA602 3.1 50.6 1.0 C4C N:HEA602 3.1 47.9 1.0 C4A N:HEA602 3.1 50.9 1.0 C1C N:HEA602 3.1 45.4 1.0 C4B N:HEA602 3.1 44.8 1.0 C4D N:HEA602 3.1 47.7 1.0 C1D N:HEA602 3.2 49.0 1.0 CD2 N:HIS376 3.2 71.2 1.0 CHB N:HEA602 3.4 51.4 1.0 CHA N:HEA602 3.4 50.1 1.0 CHC N:HEA602 3.5 43.3 1.0 CHD N:HEA602 3.5 46.2 1.0 ND1 N:HIS376 4.2 68.7 1.0 CG N:HIS376 4.3 68.8 1.0 C2B N:HEA602 4.4 51.1 1.0 C3C N:HEA602 4.4 52.4 1.0 C3A N:HEA602 4.4 54.0 1.0 C2C N:HEA602 4.4 49.6 1.0 C3B N:HEA602 4.4 50.2 1.0 C3D N:HEA602 4.4 49.0 1.0 C2A N:HEA602 4.4 52.7 1.0 C2D N:HEA602 4.5 47.6 1.0

I.Ishigami, A.Lewis-Ballester, A.Echelmeier, G.Brehm, N.A.Zatsepin, T.D.Grant, J.D.Coe, S.Lisova, G.Nelson, S.Zhang, Z.F.Dobson, S.Boutet, R.G.Sierra, A.Batyuk, P.Fromme, R.Fromme, J.C.H.Spence, A.Ros, S.R.Yeh, D.L.Rousseau. Snapshot of An Oxygen Intermediate in the Catalytic Reaction of Cytochromecoxidase. Proc. Natl. Acad. Sci. V. 116 3572 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30808749
DOI: 10.1073/PNAS.1814526116