Atomistry » Iron » PDB 8gdi-8hbh » 8h8r
Atomistry »
  Iron »
    PDB 8gdi-8hbh »
      8h8r »

Iron in PDB 8h8r: Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State

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

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State, PDB code: 8h8r was solved by K.Muramoto, K.Shinzawa-Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.8, 205.7, 177.9, 90, 90, 90
R / Rfree (%) 12.2 / 15.3

Other elements in 8h8r:

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

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

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Oxidized State (pdb code 8h8r). 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 Calcium-Bound Fully Oxidized State, PDB code: 8h8r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8h8r

Go back to Iron Binding Sites List in 8h8r
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Calcium-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 Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:27.8
occ:1.00
 FE A:HEA601 0.0 27.8 1.0
ND A:HEA601 2.0 27.3 1.0
NB A:HEA601 2.0 26.7 1.0
NC A:HEA601 2.0 26.5 1.0
NA A:HEA601 2.0 26.6 1.0
NE2 A:HIS378 2.0 27.0 1.0
NE2 A:HIS61 2.0 27.2 1.0
C1C A:HEA601 3.0 28.7 1.0
CE1 A:HIS378 3.0 29.3 1.0
C1D A:HEA601 3.0 25.4 1.0
C1B A:HEA601 3.0 26.7 1.0
C4D A:HEA601 3.0 28.0 1.0
CE1 A:HIS61 3.0 28.5 1.0
C1A A:HEA601 3.0 29.7 1.0
CD2 A:HIS61 3.1 29.2 1.0
C4C A:HEA601 3.1 26.1 1.0
C4A A:HEA601 3.1 27.3 1.0
C4B A:HEA601 3.1 28.7 1.0
CD2 A:HIS378 3.1 28.6 1.0
CHC A:HEA601 3.4 25.9 1.0
CHA A:HEA601 3.4 25.2 1.0
CHD A:HEA601 3.5 26.3 1.0
CHB A:HEA601 3.5 29.6 1.0
ND1 A:HIS378 4.1 28.1 1.0
ND1 A:HIS61 4.1 27.5 1.0
CG A:HIS61 4.2 26.5 1.0
CG A:HIS378 4.2 27.6 1.0
C3A A:HEA601 4.3 27.3 1.0
C2D A:HEA601 4.3 25.1 1.0
C2C A:HEA601 4.3 26.8 1.0
C2A A:HEA601 4.3 27.8 1.0
C3D A:HEA601 4.3 27.1 1.0
C2B A:HEA601 4.3 28.3 1.0
C3C A:HEA601 4.3 26.6 1.0
C3B A:HEA601 4.3 28.0 1.0
CE1 A:PHE377 4.9 29.6 1.0

Iron binding site 2 out of 4 in 8h8r

Go back to Iron Binding Sites List in 8h8r
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Calcium-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 Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:27.9
occ:1.00
 FE A:HEA602 0.0 27.9 1.0
ND A:HEA602 2.0 27.4 1.0
NB A:HEA602 2.0 28.1 1.0
NA A:HEA602 2.0 26.2 1.0
NC A:HEA602 2.1 26.6 1.0
NE2 A:HIS376 2.2 28.0 1.0
O1 A:PER606 2.3 29.8 1.0
C4A A:HEA602 3.0 25.8 1.0
C4D A:HEA602 3.0 27.2 1.0
C1C A:HEA602 3.0 27.9 1.0
C1A A:HEA602 3.0 27.7 1.0
C4C A:HEA602 3.0 26.6 1.0
C4B A:HEA602 3.0 28.1 1.0
C1B A:HEA602 3.1 26.4 1.0
C1D A:HEA602 3.1 26.7 1.0
CD2 A:HIS376 3.1 29.3 1.0
CE1 A:HIS376 3.2 28.7 1.0
CHA A:HEA602 3.4 26.6 1.0
CHC A:HEA602 3.4 27.9 1.0
CHD A:HEA602 3.5 26.6 1.0
CHB A:HEA602 3.5 28.4 1.0
O2 A:PER606 3.8 35.0 1.0
ND1 A:HIS376 4.3 27.1 1.0
CG A:HIS376 4.3 29.5 1.0
C3A A:HEA602 4.3 26.4 1.0
C3D A:HEA602 4.3 26.1 1.0
C2D A:HEA602 4.3 27.8 1.0
C2A A:HEA602 4.3 24.9 1.0
C3C A:HEA602 4.3 27.4 1.0
C3B A:HEA602 4.3 27.2 1.0
C2C A:HEA602 4.3 26.8 1.0
C2B A:HEA602 4.4 27.3 1.0
CU A:CU603 4.9 28.6 1.0

Iron binding site 3 out of 4 in 8h8r

Go back to Iron Binding Sites List in 8h8r
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Calcium-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 Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:35.4
occ:1.00
 FE N:HEA603 0.0 35.4 1.0
NC N:HEA603 2.0 31.6 1.0
NB N:HEA603 2.0 35.6 1.0
ND N:HEA603 2.0 33.2 1.0
NA N:HEA603 2.0 34.0 1.0
NE2 N:HIS61 2.0 34.3 1.0
NE2 N:HIS378 2.1 36.6 1.0
C1B N:HEA603 3.0 34.0 1.0
C1A N:HEA603 3.0 34.9 1.0
CD2 N:HIS61 3.0 35.9 1.0
C1D N:HEA603 3.0 33.4 1.0
C4A N:HEA603 3.0 34.2 1.0
C4C N:HEA603 3.0 34.2 1.0
C1C N:HEA603 3.0 36.3 1.0
CD2 N:HIS378 3.0 35.6 1.0
C4D N:HEA603 3.1 34.3 1.0
C4B N:HEA603 3.1 36.6 1.0
CE1 N:HIS378 3.1 33.8 1.0
CE1 N:HIS61 3.1 38.9 1.0
CHB N:HEA603 3.4 36.9 1.0
CHA N:HEA603 3.4 35.4 1.0
CHD N:HEA603 3.4 33.3 1.0
CHC N:HEA603 3.4 33.6 1.0
CG N:HIS61 4.2 35.1 1.0
ND1 N:HIS378 4.2 36.2 1.0
ND1 N:HIS61 4.2 33.5 1.0
CG N:HIS378 4.2 33.2 1.0
C3A N:HEA603 4.3 34.5 1.0
C2A N:HEA603 4.3 34.8 1.0
C2B N:HEA603 4.3 35.3 1.0
C3C N:HEA603 4.3 34.1 1.0
C2C N:HEA603 4.3 35.4 1.0
C2D N:HEA603 4.3 32.9 1.0
C3B N:HEA603 4.3 35.1 1.0
C3D N:HEA603 4.4 33.0 1.0
CE1 N:PHE377 4.9 34.5 1.0

Iron binding site 4 out of 4 in 8h8r

Go back to Iron Binding Sites List in 8h8r
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Calcium-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 Calcium-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe604

b:32.0
occ:1.00
 FE N:HEA604 0.0 32.0 1.0
NA N:HEA604 2.0 32.9 1.0
NB N:HEA604 2.0 31.6 1.0
NC N:HEA604 2.0 30.1 1.0
ND N:HEA604 2.0 31.5 1.0
NE2 N:HIS376 2.2 32.7 1.0
O1 N:PER608 2.3 33.9 1.0
C4C N:HEA604 3.0 31.9 1.0
C1A N:HEA604 3.0 32.3 1.0
C4D N:HEA604 3.0 32.2 1.0
C1C N:HEA604 3.0 31.8 1.0
C1B N:HEA604 3.1 30.8 1.0
C4B N:HEA604 3.1 32.8 1.0
C4A N:HEA604 3.1 28.4 1.0
C1D N:HEA604 3.1 33.1 1.0
CD2 N:HIS376 3.1 33.0 1.0
CE1 N:HIS376 3.2 33.7 1.0
CHA N:HEA604 3.4 31.8 1.0
CHC N:HEA604 3.4 29.8 1.0
CHD N:HEA604 3.4 31.7 1.0
CHB N:HEA604 3.5 33.3 1.0
O2 N:PER608 3.7 40.8 1.0
C3A N:HEA604 4.3 29.8 1.0
CG N:HIS376 4.3 33.7 1.0
ND1 N:HIS376 4.3 31.2 1.0
C2A N:HEA604 4.3 31.7 1.0
C3B N:HEA604 4.3 30.4 1.0
C2C N:HEA604 4.3 30.9 1.0
C3C N:HEA604 4.3 31.8 1.0
C3D N:HEA604 4.4 31.6 1.0
C2B N:HEA604 4.4 31.4 1.0
C2D N:HEA604 4.4 32.1 1.0
CU N:CU605 4.9 32.8 1.0

Reference:

K.Muramoto, K.Shinzawa-Itoh. Calcium-Bound Structure of Bovine Cytochrome C Oxidase. Biochim Biophys Acta 48956 2023BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 36708913
DOI: 10.1016/J.BBABIO.2023.148956
Page generated: Thu Aug 7 17:43:38 2025

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy