Iron in PDB 6nmp: Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature

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

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature, PDB code: 6nmp 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 / 2.90
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 (%)	19.2 / 24.4

The structure of Sfx Structure of Oxidized 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 Oxidized Cytochrome C Oxidase at Room Temperature (pdb code 6nmp). 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 Oxidized Cytochrome C Oxidase at Room Temperature, PDB code: 6nmp:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Sfx Structure of Oxidized 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 Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe604 b:34.8 occ:1.00 FE A:HEA604 0.0 34.8 1.0 NE2 A:HIS61 2.0 37.7 1.0 NE2 A:HIS378 2.0 40.2 1.0 NA A:HEA604 2.1 35.3 1.0 ND A:HEA604 2.1 34.6 1.0 NC A:HEA604 2.1 39.0 1.0 NB A:HEA604 2.1 37.3 1.0 CE1 A:HIS378 2.9 41.9 1.0 CE1 A:HIS61 3.0 37.3 1.0 C4A A:HEA604 3.0 35.0 1.0 C4C A:HEA604 3.1 40.1 1.0 CD2 A:HIS61 3.1 38.0 1.0 C1B A:HEA604 3.1 38.0 1.0 C1D A:HEA604 3.1 36.6 1.0 C4D A:HEA604 3.1 35.0 1.0 C1C A:HEA604 3.1 39.7 1.0 CD2 A:HIS378 3.1 41.4 1.0 C1A A:HEA604 3.1 33.7 1.0 C4B A:HEA604 3.2 38.7 1.0 CHB A:HEA604 3.4 36.8 1.0 CHD A:HEA604 3.4 38.1 1.0 CHC A:HEA604 3.5 39.6 1.0 CHA A:HEA604 3.5 34.4 1.0 ND1 A:HIS378 4.1 40.6 1.0 ND1 A:HIS61 4.1 36.4 1.0 CG A:HIS61 4.2 36.8 1.0 CG A:HIS378 4.2 40.8 1.0 C3A A:HEA604 4.3 34.4 1.0 C3C A:HEA604 4.4 41.3 1.0 C2A A:HEA604 4.4 33.0 1.0 C2C A:HEA604 4.4 41.4 1.0 C3D A:HEA604 4.4 38.6 1.0 C2D A:HEA604 4.4 37.8 1.0 C2B A:HEA604 4.4 39.2 1.0 C3B A:HEA604 4.5 38.5 1.0 CE1 A:PHE377 5.0 37.3 1.0

Iron binding site 2 out of 4 in the Sfx Structure of Oxidized 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 Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe605 b:35.5 occ:1.00 FE A:HEA605 0.0 35.5 1.0 O2 A:PER609 2.0 38.4 1.0 NB A:HEA605 2.1 32.4 1.0 NA A:HEA605 2.1 33.9 1.0 ND A:HEA605 2.1 34.0 1.0 NC A:HEA605 2.1 34.1 1.0 NE2 A:HIS376 2.1 36.8 1.0 CE1 A:HIS376 3.0 36.0 1.0 C1B A:HEA605 3.1 32.6 1.0 C4B A:HEA605 3.1 33.7 1.0 C4A A:HEA605 3.1 34.2 1.0 C1A A:HEA605 3.1 33.9 1.0 C4D A:HEA605 3.1 35.0 1.0 C1C A:HEA605 3.1 33.7 1.0 C1D A:HEA605 3.1 34.2 1.0 C4C A:HEA605 3.1 33.2 1.0 CD2 A:HIS376 3.2 35.9 1.0 CHB A:HEA605 3.4 34.5 1.0 CHC A:HEA605 3.4 34.6 1.0 CHA A:HEA605 3.5 35.3 1.0 O1 A:PER609 3.5 38.6 1.0 CHD A:HEA605 3.5 33.9 1.0 ND1 A:HIS376 4.2 34.7 1.0 CG A:HIS376 4.3 34.9 1.0 C2B A:HEA605 4.4 32.7 1.0 C3A A:HEA605 4.4 34.3 1.0 C3B A:HEA605 4.4 33.1 1.0 C2A A:HEA605 4.4 32.9 1.0 C3C A:HEA605 4.5 32.4 1.0 C3D A:HEA605 4.5 35.9 1.0 C2C A:HEA605 4.5 32.0 1.0 C2D A:HEA605 4.5 35.6 1.0 CU A:CU601 4.9 44.3 1.0

Iron binding site 3 out of 4 in the Sfx Structure of Oxidized 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 Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe604 b:49.6 occ:1.00 FE N:HEA604 0.0 49.6 1.0 NC N:HEA604 2.1 47.2 1.0 NB N:HEA604 2.1 51.8 1.0 ND N:HEA604 2.1 50.5 1.0 NA N:HEA604 2.1 48.7 1.0 NE2 N:HIS61 2.1 57.3 1.0 NE2 N:HIS378 2.1 55.0 1.0 CE1 N:HIS378 2.9 56.4 1.0 CD2 N:HIS61 3.0 55.5 1.0 C4C N:HEA604 3.1 49.1 1.0 C1C N:HEA604 3.1 49.3 1.0 C1B N:HEA604 3.1 51.7 1.0 C4A N:HEA604 3.1 47.6 1.0 C1D N:HEA604 3.1 50.7 1.0 C4D N:HEA604 3.1 48.9 1.0 C4B N:HEA604 3.1 49.1 1.0 C1A N:HEA604 3.1 50.8 1.0 CE1 N:HIS61 3.2 57.6 1.0 CD2 N:HIS378 3.3 55.5 1.0 CHD N:HEA604 3.5 49.8 1.0 CHB N:HEA604 3.5 46.0 1.0 CHC N:HEA604 3.5 47.6 1.0 CHA N:HEA604 3.5 50.1 1.0 ND1 N:HIS378 4.1 54.8 1.0 CG N:HIS61 4.2 57.8 1.0 ND1 N:HIS61 4.2 55.0 1.0 CG N:HIS378 4.3 55.6 1.0 C3C N:HEA604 4.4 51.0 1.0 C2C N:HEA604 4.4 52.9 1.0 C3A N:HEA604 4.4 55.4 1.0 C2B N:HEA604 4.4 55.7 1.0 C2D N:HEA604 4.4 49.6 1.0 C3D N:HEA604 4.4 49.5 1.0 C3B N:HEA604 4.4 51.3 1.0 C2A N:HEA604 4.5 54.0 1.0 O N:HOH740 4.9 0.5 1.0

Iron binding site 4 out of 4 in the Sfx Structure of Oxidized 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 Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe605 b:47.5 occ:1.00 FE N:HEA605 0.0 47.5 1.0 O1 N:PER607 2.0 53.4 1.0 NB N:HEA605 2.1 40.7 1.0 NC N:HEA605 2.1 43.0 1.0 NA N:HEA605 2.1 43.0 1.0 ND N:HEA605 2.1 44.5 1.0 NE2 N:HIS376 2.2 53.2 1.0 C1B N:HEA605 3.0 42.6 1.0 C4B N:HEA605 3.1 39.5 1.0 C4C N:HEA605 3.1 42.9 1.0 C1C N:HEA605 3.1 42.0 1.0 C4A N:HEA605 3.1 42.9 1.0 C1A N:HEA605 3.1 42.9 1.0 C4D N:HEA605 3.1 42.6 1.0 CD2 N:HIS376 3.1 54.1 1.0 C1D N:HEA605 3.2 43.0 1.0 CE1 N:HIS376 3.2 53.7 1.0 CHB N:HEA605 3.4 42.7 1.0 CHC N:HEA605 3.4 39.6 1.0 CHA N:HEA605 3.5 42.8 1.0 CHD N:HEA605 3.5 43.1 1.0 O2 N:PER607 3.6 50.1 1.0 ND1 N:HIS376 4.3 51.6 1.0 CG N:HIS376 4.3 52.3 1.0 C2B N:HEA605 4.4 43.2 1.0 C3B N:HEA605 4.4 40.9 1.0 C3C N:HEA605 4.4 44.4 1.0 C3A N:HEA605 4.4 43.4 1.0 C2C N:HEA605 4.4 42.8 1.0 C3D N:HEA605 4.5 41.7 1.0 C2A N:HEA605 4.5 43.5 1.0 C2D N:HEA605 4.5 41.4 1.0 CU N:CU601 4.8 58.2 1.0 CG2 N:VAL243 4.8 50.7 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