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Iron in PDB 9ikh: Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State, PDB code: 9ikh was solved by K.Muramoto, T.Ide, K.Shinzawa-Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.1, 204.3, 177.8, 90, 90, 90
R / Rfree (%) 13.8 / 17.4

Other elements in 9ikh:

The structure of Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State (pdb code 9ikh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State, PDB code: 9ikh:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 9ikh

Go back to Iron Binding Sites List in 9ikh
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:29.0
occ:1.00
 FE A:HEA601 0.0 29.0 1.0
NA A:HEA601 2.0 29.2 1.0
NC A:HEA601 2.0 29.9 1.0
ND A:HEA601 2.0 29.1 1.0
NB A:HEA601 2.0 28.9 1.0
NE2 A:HIS61 2.1 27.6 1.0
NE2 A:HIS378 2.1 27.3 1.0
CE1 A:HIS378 3.0 31.1 1.0
C1D A:HEA601 3.0 28.6 1.0
C1B A:HEA601 3.0 29.6 1.0
C1C A:HEA601 3.0 29.9 1.0
C4A A:HEA601 3.0 28.8 1.0
C4D A:HEA601 3.0 28.6 1.0
CD2 A:HIS61 3.1 28.7 1.0
C1A A:HEA601 3.1 28.1 1.0
CE1 A:HIS61 3.1 29.8 1.0
C4C A:HEA601 3.1 29.0 1.0
C4B A:HEA601 3.1 28.8 1.0
CD2 A:HIS378 3.1 29.4 1.0
CHC A:HEA601 3.4 26.8 1.0
CHD A:HEA601 3.4 28.1 1.0
CHB A:HEA601 3.4 29.3 1.0
CHA A:HEA601 3.4 29.9 1.0
ND1 A:HIS378 4.2 29.5 1.0
ND1 A:HIS61 4.2 29.4 1.0
CG A:HIS61 4.2 29.2 1.0
CG A:HIS378 4.2 29.9 1.0
C3A A:HEA601 4.3 29.1 1.0
C2A A:HEA601 4.3 29.6 1.0
C2D A:HEA601 4.3 28.6 1.0
C2B A:HEA601 4.4 29.1 1.0
C3D A:HEA601 4.4 28.0 1.0
C2C A:HEA601 4.4 29.5 1.0
C3C A:HEA601 4.4 28.0 1.0
C3B A:HEA601 4.4 28.3 1.0
CE1 A:PHE377 4.9 31.8 1.0

Iron binding site 2 out of 4 in 9ikh

Go back to Iron Binding Sites List in 9ikh
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:28.9
occ:1.00
 FE A:HEA602 0.0 28.9 1.0
NA A:HEA602 2.0 29.3 1.0
NC A:HEA602 2.0 27.4 1.0
NB A:HEA602 2.0 29.3 1.0
ND A:HEA602 2.1 29.5 1.0
NE2 A:HIS376 2.2 29.8 1.0
O1 A:PER606 2.3 28.3 1.0
C4A A:HEA602 3.0 29.0 1.0
C1C A:HEA602 3.0 29.7 1.0
C1B A:HEA602 3.0 29.2 1.0
C4D A:HEA602 3.0 28.2 1.0
C1A A:HEA602 3.0 29.2 1.0
C4C A:HEA602 3.1 29.2 1.0
C1D A:HEA602 3.1 27.9 1.0
C4B A:HEA602 3.1 28.8 1.0
CD2 A:HIS376 3.2 29.3 1.0
CE1 A:HIS376 3.2 30.9 1.0
CHB A:HEA602 3.4 30.5 1.0
CHA A:HEA602 3.4 28.7 1.0
CHC A:HEA602 3.4 29.2 1.0
CHD A:HEA602 3.5 27.8 1.0
O2 A:PER606 3.6 34.9 1.0
C3A A:HEA602 4.3 28.6 1.0
ND1 A:HIS376 4.3 29.8 1.0
C2A A:HEA602 4.3 27.3 1.0
CG A:HIS376 4.3 29.4 1.0
C3C A:HEA602 4.3 27.6 1.0
C2D A:HEA602 4.3 27.5 1.0
C2C A:HEA602 4.3 29.9 1.0
C2B A:HEA602 4.3 28.5 1.0
C3D A:HEA602 4.4 27.4 1.0
C3B A:HEA602 4.4 27.6 1.0
CU A:CU603 4.9 30.0 1.0

Iron binding site 3 out of 4 in 9ikh

Go back to Iron Binding Sites List in 9ikh
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:32.5
occ:1.00
 FE N:HEA602 0.0 32.5 1.0
NA N:HEA602 2.0 32.8 1.0
NB N:HEA602 2.0 31.7 1.0
ND N:HEA602 2.0 33.2 1.0
NC N:HEA602 2.1 31.3 1.0
NE2 N:HIS61 2.1 31.2 1.0
NE2 N:HIS378 2.1 31.2 1.0
C1B N:HEA602 3.0 33.3 1.0
CD2 N:HIS61 3.0 33.9 1.0
C1A N:HEA602 3.0 32.5 1.0
C4A N:HEA602 3.0 34.1 1.0
C1D N:HEA602 3.0 31.3 1.0
C4B N:HEA602 3.0 33.9 1.0
CE1 N:HIS378 3.1 33.3 1.0
C4C N:HEA602 3.1 32.3 1.0
C4D N:HEA602 3.1 33.3 1.0
C1C N:HEA602 3.1 33.5 1.0
CE1 N:HIS61 3.1 34.4 1.0
CD2 N:HIS378 3.1 33.4 1.0
CHB N:HEA602 3.4 33.5 1.0
CHD N:HEA602 3.4 31.1 1.0
CHC N:HEA602 3.4 30.8 1.0
CHA N:HEA602 3.4 33.1 1.0
CG N:HIS61 4.2 34.5 1.0
ND1 N:HIS378 4.2 34.7 1.0
ND1 N:HIS61 4.2 32.2 1.0
CG N:HIS378 4.2 32.3 1.0
C3A N:HEA602 4.3 34.1 1.0
C2A N:HEA602 4.3 34.6 1.0
C2B N:HEA602 4.3 33.5 1.0
C3B N:HEA602 4.4 33.2 1.0
C2D N:HEA602 4.4 30.2 1.0
C3C N:HEA602 4.4 32.2 1.0
C3D N:HEA602 4.4 29.8 1.0
C2C N:HEA602 4.4 33.4 1.0
CE1 N:PHE377 4.8 34.2 1.0

Iron binding site 4 out of 4 in 9ikh

Go back to Iron Binding Sites List in 9ikh
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bovine Heart Cytochrome C Oxidase in the Nitrous Oxide-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:30.9
occ:1.00
 FE N:HEA603 0.0 30.9 1.0
NA N:HEA603 2.0 32.9 1.0
NB N:HEA603 2.0 32.6 1.0
NC N:HEA603 2.0 30.5 1.0
ND N:HEA603 2.0 31.3 1.0
NE2 N:HIS376 2.2 33.4 1.0
O1 N:PER607 2.3 32.1 1.0
C1B N:HEA603 3.0 31.4 1.0
C4B N:HEA603 3.0 30.8 1.0
C1D N:HEA603 3.0 31.1 1.0
C4D N:HEA603 3.0 31.8 1.0
C1C N:HEA603 3.0 32.0 1.0
C4A N:HEA603 3.1 29.4 1.0
C1A N:HEA603 3.1 29.7 1.0
C4C N:HEA603 3.1 33.1 1.0
CD2 N:HIS376 3.2 33.5 1.0
CE1 N:HIS376 3.2 33.7 1.0
CHC N:HEA603 3.4 30.4 1.0
CHA N:HEA603 3.4 32.6 1.0
CHB N:HEA603 3.4 31.2 1.0
CHD N:HEA603 3.4 30.9 1.0
O2 N:PER607 3.6 35.9 1.0
ND1 N:HIS376 4.3 30.7 1.0
CG N:HIS376 4.3 31.7 1.0
C3A N:HEA603 4.3 30.1 1.0
C2B N:HEA603 4.3 29.5 1.0
C2A N:HEA603 4.3 32.8 1.0
C2D N:HEA603 4.3 31.6 1.0
C3B N:HEA603 4.4 30.6 1.0
C3C N:HEA603 4.4 32.9 1.0
C2C N:HEA603 4.4 30.7 1.0
C3D N:HEA603 4.4 31.1 1.0
CU N:CU604 4.9 31.9 1.0

Reference:

K.Muramoto, T.Ide, K.Shinzawa-Itoh. The Binding Sites of Carbon Dioxide, Nitrous Oxide, and Xenon Reveal A Putative Exhaust Channel For Bovine Cytochrome C Oxidase. J.Biol.Chem. 10395 2025.
ISSN: ESSN 1083-351X
PubMed: 40543594
DOI: 10.1016/J.JBC.2025.110395
Page generated: Fri Aug 8 06:50:37 2025

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