Iron in PDB 6pw0: Cytochrome C Oxidase Delta 6 Mutant

All present enzymatic activity of Cytochrome C Oxidase Delta 6 Mutant:
1.9.3.1;

The structure of Cytochrome C Oxidase Delta 6 Mutant, PDB code: 6pw0 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)	42.84 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	124.905, 131.477, 176.601, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.8

The structure of Cytochrome C Oxidase Delta 6 Mutant 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 6 Mutant (pdb code 6pw0). 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 6 Mutant, PDB code: 6pw0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:31.9 occ:1.00 FE A:HEA602 0.0 31.9 1.0 NA A:HEA602 2.0 37.6 1.0 NB A:HEA602 2.1 30.5 1.0 NC A:HEA602 2.1 37.0 1.0 ND A:HEA602 2.1 32.3 1.0 NE2 A:HIS102 2.2 27.5 1.0 NE2 A:HIS421 2.2 30.4 1.0 C4A A:HEA602 3.0 30.3 1.0 C1A A:HEA602 3.1 31.9 1.0 C4B A:HEA602 3.1 33.1 1.0 C4C A:HEA602 3.1 32.6 1.0 C1B A:HEA602 3.1 33.8 1.0 C1C A:HEA602 3.1 34.1 1.0 C1D A:HEA602 3.1 32.6 1.0 C4D A:HEA602 3.1 29.6 1.0 CD2 A:HIS102 3.2 29.5 1.0 CE1 A:HIS421 3.2 31.9 1.0 CE1 A:HIS102 3.2 32.4 1.0 CD2 A:HIS421 3.3 34.1 1.0 CHC A:HEA602 3.5 29.8 1.0 CHA A:HEA602 3.5 30.7 1.0 CHB A:HEA602 3.5 32.0 1.0 CHD A:HEA602 3.5 31.4 1.0 C3A A:HEA602 4.3 32.3 1.0 C2A A:HEA602 4.3 30.4 1.0 ND1 A:HIS421 4.3 35.3 1.0 CG A:HIS102 4.3 32.3 1.0 ND1 A:HIS102 4.3 31.9 1.0 CG A:HIS421 4.4 34.9 1.0 C3B A:HEA602 4.4 33.0 1.0 C3C A:HEA602 4.4 33.0 1.0 C2B A:HEA602 4.4 34.7 1.0 C2C A:HEA602 4.5 33.2 1.0 C3D A:HEA602 4.5 35.2 1.0 C2D A:HEA602 4.5 37.4 1.0 CG2 A:THR48 4.6 31.6 1.0 CE1 A:PHE420 5.0 32.6 1.0

Iron binding site 2 out of 4 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:36.1 occ:1.00 FE A:HEA603 0.0 36.1 1.0 NA A:HEA603 2.0 41.2 1.0 ND A:HEA603 2.1 34.9 1.0 NC A:HEA603 2.1 40.3 1.0 NB A:HEA603 2.1 39.5 1.0 NE2 A:HIS419 2.3 30.5 1.0 O A:HOH701 2.5 34.2 1.0 C4A A:HEA603 3.1 32.1 1.0 C1A A:HEA603 3.1 29.6 1.0 C1C A:HEA603 3.1 33.6 1.0 C1D A:HEA603 3.1 38.8 1.0 C4D A:HEA603 3.1 30.5 1.0 C4C A:HEA603 3.1 35.9 1.0 C4B A:HEA603 3.1 38.8 1.0 C1B A:HEA603 3.2 41.3 1.0 CE1 A:HIS419 3.3 39.5 1.0 CD2 A:HIS419 3.3 36.0 1.0 CHC A:HEA603 3.5 36.2 1.0 CHD A:HEA603 3.5 33.1 1.0 CHA A:HEA603 3.5 33.3 1.0 CHB A:HEA603 3.5 33.0 1.0 O A:OH601 4.3 40.4 1.0 C3A A:HEA603 4.3 38.4 1.0 C2A A:HEA603 4.4 38.5 1.0 ND1 A:HIS419 4.4 36.5 1.0 C3C A:HEA603 4.4 38.0 1.0 C2D A:HEA603 4.4 33.0 1.0 C3D A:HEA603 4.4 34.0 1.0 C2C A:HEA603 4.5 35.9 1.0 CG A:HIS419 4.5 34.7 1.0 C3B A:HEA603 4.5 42.2 1.0 C2B A:HEA603 4.5 39.9 1.0 CU A:CU617 4.8 38.4 1.0

Iron binding site 3 out of 4 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe602 b:42.2 occ:1.00 FE C:HEA602 0.0 42.2 1.0 NA C:HEA602 2.0 47.3 1.0 ND C:HEA602 2.1 44.3 1.0 NB C:HEA602 2.1 40.5 1.0 NC C:HEA602 2.1 46.5 1.0 NE2 C:HIS421 2.3 41.4 1.0 NE2 C:HIS102 2.3 46.2 1.0 C1A C:HEA602 3.0 35.2 1.0 C4A C:HEA602 3.1 38.2 1.0 C4B C:HEA602 3.1 46.0 1.0 C1D C:HEA602 3.1 41.5 1.0 C4C C:HEA602 3.1 38.2 1.0 C4D C:HEA602 3.1 45.5 1.0 C1C C:HEA602 3.1 40.3 1.0 C1B C:HEA602 3.1 45.5 1.0 CD2 C:HIS102 3.2 45.9 1.0 CE1 C:HIS421 3.2 44.5 1.0 CD2 C:HIS421 3.3 43.5 1.0 CE1 C:HIS102 3.3 46.5 1.0 CHA C:HEA602 3.5 41.3 1.0 CHC C:HEA602 3.5 41.0 1.0 CHD C:HEA602 3.5 44.1 1.0 CHB C:HEA602 3.5 39.4 1.0 C3A C:HEA602 4.3 42.0 1.0 C2A C:HEA602 4.3 45.2 1.0 ND1 C:HIS421 4.4 43.9 1.0 CG C:HIS102 4.4 51.6 1.0 ND1 C:HIS102 4.4 57.3 1.0 CG C:HIS421 4.4 41.9 1.0 C3C C:HEA602 4.4 41.5 1.0 C3B C:HEA602 4.4 44.2 1.0 C2D C:HEA602 4.4 39.2 1.0 C3D C:HEA602 4.5 41.4 1.0 C2B C:HEA602 4.5 39.9 1.0 C2C C:HEA602 4.5 49.4 1.0 CG2 C:THR48 4.7 43.4 1.0

Iron binding site 4 out of 4 in the Cytochrome C Oxidase Delta 6 Mutant


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 6 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe603 b:42.3 occ:1.00 FE C:HEA603 0.0 42.3 1.0 NA C:HEA603 2.0 47.8 1.0 ND C:HEA603 2.1 48.3 1.0 NB C:HEA603 2.1 50.1 1.0 NC C:HEA603 2.1 49.8 1.0 NE2 C:HIS419 2.3 40.9 1.0 O C:HOH701 2.4 38.8 1.0 C1A C:HEA603 3.1 38.2 1.0 C4A C:HEA603 3.1 44.2 1.0 C4D C:HEA603 3.1 42.0 1.0 C4B C:HEA603 3.1 46.2 1.0 C1D C:HEA603 3.1 49.0 1.0 C1C C:HEA603 3.1 44.5 1.0 C4C C:HEA603 3.1 49.1 1.0 C1B C:HEA603 3.2 47.8 1.0 CD2 C:HIS419 3.3 44.1 1.0 CE1 C:HIS419 3.4 43.4 1.0 CHA C:HEA603 3.5 42.7 1.0 CHC C:HEA603 3.5 45.4 1.0 CHB C:HEA603 3.5 48.3 1.0 CHD C:HEA603 3.5 44.9 1.0 O C:OH601 4.0 48.5 1.0 C3A C:HEA603 4.3 39.1 1.0 C2A C:HEA603 4.3 41.1 1.0 CG C:HIS419 4.4 40.9 1.0 C3D C:HEA603 4.4 43.4 1.0 ND1 C:HIS419 4.5 42.2 1.0 C3C C:HEA603 4.5 46.2 1.0 C3B C:HEA603 4.5 47.6 1.0 C2D C:HEA603 4.5 44.4 1.0 C2B C:HEA603 4.5 41.6 1.0 C2C C:HEA603 4.5 45.3 1.0 CU C:CU609 4.8 44.9 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