Iron in PDB 6pw1: Cytochrome C Oxidase Delta 16

All present enzymatic activity of Cytochrome C Oxidase Delta 16:
1.9.3.1;

The structure of Cytochrome C Oxidase Delta 16, PDB code: 6pw1 was solved by J.Liu, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.96 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	123.315, 130.000, 177.539, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.4

The structure of Cytochrome C Oxidase Delta 16 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Cadmium	(Cd)	4 atoms
Calcium	(Ca)	2 atoms
Copper	(Cu)	6 atoms

The binding sites of Iron atom in the Cytochrome C Oxidase Delta 16 (pdb code 6pw1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cytochrome C Oxidase Delta 16, PDB code: 6pw1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe615 b:24.8 occ:1.00 FE A:HEA615 0.0 24.8 1.0 NA A:HEA615 2.0 28.3 1.0 ND A:HEA615 2.1 27.6 1.0 NC A:HEA615 2.1 26.0 1.0 NB A:HEA615 2.1 26.2 1.0 NE2 A:HIS421 2.1 23.2 1.0 NE2 A:HIS102 2.2 25.2 1.0 CE1 A:HIS421 3.0 24.2 1.0 C1A A:HEA615 3.1 24.5 1.0 C4A A:HEA615 3.1 25.3 1.0 C4D A:HEA615 3.1 23.6 1.0 C4C A:HEA615 3.1 25.4 1.0 C4B A:HEA615 3.1 24.9 1.0 CD2 A:HIS102 3.1 23.2 1.0 C1D A:HEA615 3.1 25.1 1.0 C1B A:HEA615 3.1 24.0 1.0 C1C A:HEA615 3.1 23.2 1.0 CD2 A:HIS421 3.2 24.5 1.0 CE1 A:HIS102 3.2 26.1 1.0 CHA A:HEA615 3.5 21.2 1.0 CHC A:HEA615 3.5 21.9 1.0 CHD A:HEA615 3.5 23.8 1.0 CHB A:HEA615 3.5 23.7 1.0 ND1 A:HIS421 4.2 24.6 1.0 CG A:HIS102 4.3 25.4 1.0 ND1 A:HIS102 4.3 25.5 1.0 CG A:HIS421 4.3 25.5 1.0 C3A A:HEA615 4.3 22.3 1.0 C2A A:HEA615 4.3 23.5 1.0 C3C A:HEA615 4.4 22.8 1.0 C3D A:HEA615 4.4 23.2 1.0 C3B A:HEA615 4.4 25.9 1.0 C2D A:HEA615 4.4 24.7 1.0 C2B A:HEA615 4.4 24.8 1.0 C2C A:HEA615 4.4 25.0 1.0 CG2 A:THR48 4.6 22.8 1.0 CE1 A:PHE420 4.8 25.0 1.0

Iron binding site 2 out of 4 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe616 b:27.1 occ:1.00 FE A:HEA616 0.0 27.1 1.0 NA A:HEA616 2.0 30.2 1.0 NC A:HEA616 2.1 27.9 1.0 NB A:HEA616 2.1 31.1 1.0 ND A:HEA616 2.1 27.4 1.0 NE2 A:HIS419 2.2 25.9 1.0 O A:HOH770 2.3 23.4 1.0 C1A A:HEA616 3.1 28.6 1.0 C1C A:HEA616 3.1 25.9 1.0 C4A A:HEA616 3.1 26.8 1.0 C4D A:HEA616 3.1 26.2 1.0 C4B A:HEA616 3.1 29.3 1.0 C4C A:HEA616 3.1 27.8 1.0 C1B A:HEA616 3.1 28.9 1.0 C1D A:HEA616 3.1 27.1 1.0 CE1 A:HIS419 3.2 24.8 1.0 CD2 A:HIS419 3.2 27.6 1.0 CHC A:HEA616 3.4 24.9 1.0 CHA A:HEA616 3.5 26.1 1.0 CHB A:HEA616 3.5 25.9 1.0 CHD A:HEA616 3.5 23.8 1.0 O A:HOH830 3.9 26.9 1.0 ND1 A:HIS419 4.3 26.5 1.0 CG A:HIS419 4.3 23.5 1.0 C3A A:HEA616 4.3 27.0 1.0 C2A A:HEA616 4.4 27.9 1.0 C3C A:HEA616 4.4 24.7 1.0 C2C A:HEA616 4.4 26.3 1.0 C3D A:HEA616 4.4 24.6 1.0 C2B A:HEA616 4.4 26.7 1.0 C3B A:HEA616 4.4 29.7 1.0 C2D A:HEA616 4.5 23.3 1.0 CU A:CU617 4.8 30.6 1.0

Iron binding site 3 out of 4 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe604 b:30.3 occ:1.00 FE C:HEA604 0.0 30.3 1.0 NA C:HEA604 2.0 31.2 1.0 NB C:HEA604 2.1 29.9 1.0 ND C:HEA604 2.1 29.4 1.0 NC C:HEA604 2.1 32.2 1.0 NE2 C:HIS102 2.1 28.6 1.0 NE2 C:HIS421 2.2 28.3 1.0 C1A C:HEA604 3.1 26.7 1.0 C4A C:HEA604 3.1 28.2 1.0 C4B C:HEA604 3.1 30.2 1.0 CD2 C:HIS102 3.1 31.1 1.0 CE1 C:HIS421 3.1 29.6 1.0 C4D C:HEA604 3.1 31.7 1.0 C4C C:HEA604 3.1 29.5 1.0 C1B C:HEA604 3.1 29.1 1.0 C1D C:HEA604 3.1 31.5 1.0 C1C C:HEA604 3.1 28.8 1.0 CE1 C:HIS102 3.1 32.1 1.0 CD2 C:HIS421 3.2 28.3 1.0 CHC C:HEA604 3.5 27.4 1.0 CHA C:HEA604 3.5 25.4 1.0 CHD C:HEA604 3.5 29.3 1.0 CHB C:HEA604 3.5 24.6 1.0 ND1 C:HIS421 4.2 28.4 1.0 ND1 C:HIS102 4.2 34.4 1.0 CG C:HIS102 4.3 32.7 1.0 CG C:HIS421 4.3 31.1 1.0 C3A C:HEA604 4.3 29.0 1.0 C2A C:HEA604 4.3 28.3 1.0 C3B C:HEA604 4.4 34.2 1.0 C3C C:HEA604 4.4 28.8 1.0 C3D C:HEA604 4.4 31.1 1.0 C2B C:HEA604 4.4 28.6 1.0 C2D C:HEA604 4.4 26.0 1.0 C2C C:HEA604 4.5 31.2 1.0 CG2 C:THR48 4.6 28.1 1.0 CE1 C:PHE420 4.8 27.2 1.0

Iron binding site 4 out of 4 in the Cytochrome C Oxidase Delta 16


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome C Oxidase Delta 16 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe605 b:31.8 occ:1.00 FE C:HEA605 0.0 31.8 1.0 NA C:HEA605 2.0 33.5 1.0 NC C:HEA605 2.1 30.8 1.0 ND C:HEA605 2.1 30.5 1.0 NB C:HEA605 2.1 35.2 1.0 NE2 C:HIS419 2.3 31.2 1.0 O C:HOH740 2.3 27.9 1.0 C1A C:HEA605 3.0 29.8 1.0 C4A C:HEA605 3.1 32.3 1.0 C1C C:HEA605 3.1 29.0 1.0 C4D C:HEA605 3.1 28.9 1.0 C4C C:HEA605 3.1 31.0 1.0 C4B C:HEA605 3.1 30.6 1.0 C1D C:HEA605 3.1 32.6 1.0 C1B C:HEA605 3.2 32.5 1.0 CD2 C:HIS419 3.2 28.9 1.0 CE1 C:HIS419 3.3 32.4 1.0 CHC C:HEA605 3.4 27.6 1.0 CHA C:HEA605 3.5 27.3 1.0 CHD C:HEA605 3.5 28.0 1.0 CHB C:HEA605 3.5 33.6 1.0 O C:HOH790 3.9 32.4 1.0 C3A C:HEA605 4.3 31.4 1.0 C2A C:HEA605 4.3 31.1 1.0 ND1 C:HIS419 4.4 27.8 1.0 CG C:HIS419 4.4 28.7 1.0 C3C C:HEA605 4.4 33.3 1.0 C3D C:HEA605 4.4 31.8 1.0 C2C C:HEA605 4.4 33.5 1.0 C2D C:HEA605 4.5 27.3 1.0 C3B C:HEA605 4.5 34.2 1.0 C2B C:HEA605 4.5 31.4 1.0 CU C:CU606 4.8 34.4 1.0

J.Berg, J.Liu, E.Svahn, S.Ferguson-Miller, P.Brzezinski. Structural Changes at the Surface of Cytochrome C Oxidase Alter the Proton-Pumping Stoichiometry. Biochim Biophys Acta 48116 2019BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 31733183
DOI: 10.1016/J.BBABIO.2019.148116