Iron in PDB 5weh: Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State

All present enzymatic activity of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State:
1.9.3.1;

The structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 5weh was solved by J.Liu, F.Ferguson-Miller, Q.Ling, C.Hiser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.45 / 3.45
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	339.221, 339.221, 89.199, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 26.2

The structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	2 atoms
Copper	(Cu)	6 atoms

The binding sites of Iron atom in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State (pdb code 5weh). 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 From Rhodobacter Sphaeroides in the Reduced State, PDB code: 5weh:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State


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 From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:0.1 occ:1.00 FE A:HEA601 0.0 0.1 1.0 NA A:HEA601 1.8 0.1 1.0 ND A:HEA601 2.1 0.2 1.0 NC A:HEA601 2.1 98.4 1.0 NB A:HEA601 2.1 0.3 1.0 NE2 A:HIS421 2.2 0.4 1.0 NE2 A:HIS102 2.5 90.2 1.0 CD2 A:HIS421 3.0 0.1 1.0 C4A A:HEA601 3.0 0.8 1.0 C1A A:HEA601 3.1 0.3 1.0 C4C A:HEA601 3.2 0.2 1.0 C1D A:HEA601 3.2 0.7 1.0 CE1 A:HIS421 3.3 0.6 1.0 C1C A:HEA601 3.3 96.3 1.0 C4D A:HEA601 3.3 98.6 1.0 C1B A:HEA601 3.3 0.5 1.0 CD2 A:HIS102 3.3 97.7 1.0 C4B A:HEA601 3.4 0.9 1.0 CE1 A:HIS102 3.5 91.5 1.0 CHB A:HEA601 4.0 0.4 1.0 CHA A:HEA601 4.0 0.5 1.0 CHD A:HEA601 4.0 0.9 1.0 CG A:HIS421 4.2 0.8 1.0 CHC A:HEA601 4.2 98.7 1.0 ND1 A:HIS421 4.3 1.0 1.0 C3A A:HEA601 4.4 1.0 1.0 OG A:SER425 4.4 95.2 1.0 C2A A:HEA601 4.5 0.1 1.0 C3C A:HEA601 4.5 99.6 1.0 C2C A:HEA601 4.5 96.9 1.0 C2D A:HEA601 4.5 96.3 1.0 CG A:HIS102 4.5 0.1 1.0 C3D A:HEA601 4.6 99.0 1.0 ND1 A:HIS102 4.6 0.6 1.0 CE1 A:PHE420 4.6 0.3 1.0 C2B A:HEA601 4.7 99.8 1.0 C3B A:HEA601 4.7 0.1 1.0 CG2 A:THR48 5.0 0.9 1.0

Iron binding site 2 out of 4 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State


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 From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:0.5 occ:1.00 FE A:HEA602 0.0 0.5 1.0 NA A:HEA602 1.8 99.8 1.0 NB A:HEA602 2.1 97.7 1.0 NC A:HEA602 2.2 98.8 1.0 ND A:HEA602 2.2 95.8 1.0 NE2 A:HIS419 2.4 94.5 1.0 C4A A:HEA602 3.0 95.0 1.0 C1A A:HEA602 3.1 97.1 1.0 C1B A:HEA602 3.1 94.2 1.0 CE1 A:HIS419 3.1 0.7 1.0 C4D A:HEA602 3.2 96.1 1.0 C1C A:HEA602 3.3 99.0 1.0 C4C A:HEA602 3.3 98.5 1.0 C1D A:HEA602 3.4 95.8 1.0 C4B A:HEA602 3.5 100.0 1.0 CD2 A:HIS419 3.6 0.6 1.0 CHB A:HEA602 3.7 93.7 1.0 CHA A:HEA602 3.8 98.5 1.0 CHC A:HEA602 4.2 98.5 1.0 CHD A:HEA602 4.3 98.6 1.0 ND1 A:HIS419 4.3 1.0 1.0 C3A A:HEA602 4.4 92.4 1.0 C2A A:HEA602 4.4 94.2 1.0 C2B A:HEA602 4.5 94.6 1.0 C2C A:HEA602 4.5 0.1 1.0 C3C A:HEA602 4.5 98.0 1.0 CG A:HIS419 4.6 0.8 1.0 C3D A:HEA602 4.7 96.2 1.0 C3B A:HEA602 4.7 98.3 1.0 C2D A:HEA602 4.7 94.9 1.0 CG1 A:VAL423 4.9 0.6 1.0 CA A:GLY398 5.0 98.8 1.0

Iron binding site 3 out of 4 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State


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 From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe602 b:94.3 occ:1.00 FE G:HEA602 0.0 94.3 1.0 NA G:HEA602 1.8 0.9 1.0 ND G:HEA602 2.1 92.1 1.0 NC G:HEA602 2.2 0.7 1.0 NB G:HEA602 2.2 91.7 1.0 NE2 G:HIS421 2.4 0.0 1.0 NE2 G:HIS102 2.4 83.1 1.0 C4A G:HEA602 3.1 0.7 1.0 C1A G:HEA602 3.1 0.9 1.0 C4D G:HEA602 3.2 97.5 1.0 CD2 G:HIS421 3.2 0.3 1.0 C1D G:HEA602 3.3 96.2 1.0 CE1 G:HIS421 3.3 0.5 1.0 CD2 G:HIS102 3.3 95.6 1.0 C4C G:HEA602 3.3 0.5 1.0 C1B G:HEA602 3.3 98.3 1.0 C1C G:HEA602 3.4 93.8 1.0 C4B G:HEA602 3.4 95.4 1.0 CE1 G:HIS102 3.4 89.8 1.0 CHA G:HEA602 3.8 0.9 1.0 CHB G:HEA602 4.0 0.6 1.0 CHD G:HEA602 4.0 96.2 1.0 CHC G:HEA602 4.3 94.8 1.0 CG G:HIS421 4.3 0.8 1.0 ND1 G:HIS421 4.3 0.7 1.0 OG G:SER425 4.4 94.6 1.0 C3D G:HEA602 4.5 99.9 1.0 CG G:HIS102 4.5 0.1 1.0 C3A G:HEA602 4.5 97.2 1.0 CE1 G:PHE420 4.5 86.7 1.0 ND1 G:HIS102 4.5 96.0 1.0 C2A G:HEA602 4.5 96.8 1.0 C2D G:HEA602 4.5 97.5 1.0 C3C G:HEA602 4.6 92.0 1.0 C2C G:HEA602 4.6 89.3 1.0 C2B G:HEA602 4.7 95.8 1.0 C3B G:HEA602 4.7 95.1 1.0

Iron binding site 4 out of 4 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State


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 From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe603 b:0.5 occ:1.00 FE G:HEA603 0.0 0.5 1.0 NA G:HEA603 1.8 0.7 1.0 NB G:HEA603 2.1 0.8 1.0 NC G:HEA603 2.1 0.1 1.0 ND G:HEA603 2.2 99.4 1.0 NE2 G:HIS419 2.7 1.0 1.0 C4A G:HEA603 2.9 0.3 1.0 C1A G:HEA603 3.1 0.4 1.0 C1C G:HEA603 3.2 98.8 1.0 C1B G:HEA603 3.2 0.9 1.0 C4B G:HEA603 3.3 1.0 1.0 C4D G:HEA603 3.3 0.7 1.0 C4C G:HEA603 3.3 1.0 1.0 CE1 G:HIS419 3.4 0.6 1.0 C1D G:HEA603 3.5 97.6 1.0 CHB G:HEA603 3.8 0.1 1.0 CD2 G:HIS419 3.9 0.3 1.0 CHC G:HEA603 4.0 0.8 1.0 CHA G:HEA603 4.0 0.4 1.0 C3A G:HEA603 4.3 1.0 1.0 CHD G:HEA603 4.3 97.6 1.0 C2A G:HEA603 4.4 0.4 1.0 CU G:CU1604 4.4 94.1 1.0 C2C G:HEA603 4.5 99.0 1.0 C3C G:HEA603 4.5 97.1 1.0 C2B G:HEA603 4.6 0.8 1.0 C3B G:HEA603 4.6 0.3 1.0 ND1 G:HIS419 4.7 92.0 1.0 C3D G:HEA603 4.7 99.5 1.0 C2D G:HEA603 4.8 97.7 1.0 CG G:HIS419 4.9 95.7 1.0 NE2 G:HIS333 5.0 0.7 1.0 CE1 G:HIS284 5.0 0.3 1.0

J.Liu, C.Hiser, S.Ferguson-Miller. Role of Conformational Change and K-Path Ligands in Controlling Cytochrome C Oxidase Activity. Biochem. Soc. Trans. V. 45 1087 2017.
ISSN: ISSN 1470-8752
PubMed: 28842531
DOI: 10.1042/BST20160138