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Iron in PDB 2eik: Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

Enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

All present enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State:
1.9.3.1;

Protein crystallography data

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik was solved by K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.321, 206.525, 178.159, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 22.8

Other elements in 2eik:

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 2eik). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2eik

Go back to Iron Binding Sites List in 2eik
Iron binding site 1 out of 4 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:17.8
occ:1.00
 FE A:HEA515 0.0 17.8 1.0
NE2 A:HIS378 1.8 14.2 1.0
NB A:HEA515 1.9 20.8 1.0
NC A:HEA515 2.0 21.4 1.0
NE2 A:HIS61 2.0 14.9 1.0
NA A:HEA515 2.0 23.1 1.0
ND A:HEA515 2.0 20.3 1.0
CE1 A:HIS378 2.8 16.2 1.0
C4B A:HEA515 2.9 22.3 1.0
C1B A:HEA515 2.9 22.1 1.0
CD2 A:HIS378 3.0 13.4 1.0
CE1 A:HIS61 3.0 19.3 1.0
C4C A:HEA515 3.0 21.1 1.0
C1C A:HEA515 3.1 19.8 1.0
C4A A:HEA515 3.1 21.1 1.0
CD2 A:HIS61 3.1 17.0 1.0
C1D A:HEA515 3.1 23.1 1.0
C1A A:HEA515 3.1 20.3 1.0
C4D A:HEA515 3.1 21.1 1.0
CHB A:HEA515 3.4 17.4 1.0
CHC A:HEA515 3.4 21.3 1.0
CHD A:HEA515 3.4 17.0 1.0
CHA A:HEA515 3.5 19.5 1.0
ND1 A:HIS378 4.0 13.5 1.0
CG A:HIS378 4.1 15.8 1.0
C3B A:HEA515 4.1 22.1 1.0
C2B A:HEA515 4.2 17.5 1.0
ND1 A:HIS61 4.2 15.6 1.0
CG A:HIS61 4.2 16.6 1.0
C3C A:HEA515 4.3 19.9 1.0
C2A A:HEA515 4.3 22.4 1.0
C3A A:HEA515 4.3 21.6 1.0
C2C A:HEA515 4.3 20.7 1.0
C2D A:HEA515 4.3 19.4 1.0
C3D A:HEA515 4.3 22.3 1.0
OG A:SER382 4.6 47.4 1.0
CE2 A:PHE377 4.9 18.3 1.0

Iron binding site 2 out of 4 in 2eik

Go back to Iron Binding Sites List in 2eik
Iron binding site 2 out of 4 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:19.3
occ:1.00
 FE A:HEA516 0.0 19.3 1.0
ND A:HEA516 1.9 19.4 1.0
NB A:HEA516 1.9 19.2 1.0
NE2 A:HIS376 2.0 15.8 1.0
NA A:HEA516 2.1 18.9 1.0
NC A:HEA516 2.1 18.9 1.0
CE1 A:HIS376 2.9 20.7 1.0
C4D A:HEA516 3.0 21.4 1.0
C4B A:HEA516 3.0 23.2 1.0
C1B A:HEA516 3.0 22.4 1.0
C1D A:HEA516 3.0 21.3 1.0
C1A A:HEA516 3.1 16.5 1.0
C1C A:HEA516 3.1 18.8 1.0
C4A A:HEA516 3.1 18.8 1.0
C4C A:HEA516 3.1 19.1 1.0
CD2 A:HIS376 3.2 20.3 1.0
CHC A:HEA516 3.4 20.1 1.0
CHA A:HEA516 3.4 15.9 1.0
CHB A:HEA516 3.5 20.4 1.0
CHD A:HEA516 3.5 17.6 1.0
ND1 A:HIS376 4.2 22.0 1.0
C3D A:HEA516 4.2 17.2 1.0
C2D A:HEA516 4.2 17.9 1.0
C2B A:HEA516 4.2 19.1 1.0
C3B A:HEA516 4.2 21.1 1.0
CG A:HIS376 4.3 17.8 1.0
C2A A:HEA516 4.3 16.6 1.0
C3A A:HEA516 4.4 18.8 1.0
C2C A:HEA516 4.4 22.5 1.0
C3C A:HEA516 4.4 20.5 1.0
CG2 A:VAL380 4.8 27.2 1.0

Iron binding site 3 out of 4 in 2eik

Go back to Iron Binding Sites List in 2eik
Iron binding site 3 out of 4 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:24.5
occ:1.00
 FE N:HEA515 0.0 24.5 1.0
NB N:HEA515 1.9 26.5 1.0
NE2 N:HIS61 2.0 25.4 1.0
NA N:HEA515 2.0 22.8 1.0
NC N:HEA515 2.0 21.5 1.0
ND N:HEA515 2.0 24.2 1.0
NE2 N:HIS378 2.1 25.1 1.0
CD2 N:HIS61 2.9 24.9 1.0
C1B N:HEA515 3.0 22.9 1.0
C4B N:HEA515 3.0 24.5 1.0
CE1 N:HIS378 3.0 23.0 1.0
C4A N:HEA515 3.0 23.2 1.0
C4C N:HEA515 3.0 25.5 1.0
C1A N:HEA515 3.0 25.1 1.0
CE1 N:HIS61 3.0 29.8 1.0
C4D N:HEA515 3.1 23.6 1.0
C1C N:HEA515 3.1 23.2 1.0
C1D N:HEA515 3.1 25.1 1.0
CD2 N:HIS378 3.2 19.7 1.0
CHB N:HEA515 3.4 21.1 1.0
CHC N:HEA515 3.4 22.0 1.0
CHA N:HEA515 3.4 23.6 1.0
CHD N:HEA515 3.4 22.1 1.0
CG N:HIS61 4.1 27.6 1.0
ND1 N:HIS61 4.1 25.8 1.0
C3B N:HEA515 4.2 27.4 1.0
C2B N:HEA515 4.2 23.5 1.0
ND1 N:HIS378 4.2 21.5 1.0
C2A N:HEA515 4.2 23.6 1.0
C3A N:HEA515 4.3 24.4 1.0
CG N:HIS378 4.3 21.8 1.0
C3C N:HEA515 4.3 20.7 1.0
C3D N:HEA515 4.3 24.4 1.0
C2D N:HEA515 4.3 23.6 1.0
C2C N:HEA515 4.3 20.7 1.0
OG N:SER382 4.6 50.9 1.0
CE2 N:PHE377 5.0 20.0 1.0

Iron binding site 4 out of 4 in 2eik

Go back to Iron Binding Sites List in 2eik
Iron binding site 4 out of 4 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:22.6
occ:1.00
 FE N:HEA516 0.0 22.6 1.0
ND N:HEA516 1.9 21.8 1.0
NB N:HEA516 2.0 21.5 1.0
NC N:HEA516 2.0 20.1 1.0
NA N:HEA516 2.1 21.9 1.0
NE2 N:HIS376 2.1 26.8 1.0
C4D N:HEA516 3.0 20.4 1.0
C1D N:HEA516 3.0 21.6 1.0
C4B N:HEA516 3.0 20.4 1.0
C1B N:HEA516 3.1 22.7 1.0
C4C N:HEA516 3.1 23.2 1.0
CE1 N:HIS376 3.1 30.5 1.0
C1C N:HEA516 3.1 21.3 1.0
C1A N:HEA516 3.1 21.7 1.0
C4A N:HEA516 3.2 22.9 1.0
CD2 N:HIS376 3.2 25.6 1.0
CHD N:HEA516 3.4 23.1 1.0
CHA N:HEA516 3.4 18.4 1.0
CHC N:HEA516 3.5 21.4 1.0
CHB N:HEA516 3.5 23.4 1.0
C3D N:HEA516 4.2 21.9 1.0
C2D N:HEA516 4.2 19.7 1.0
ND1 N:HIS376 4.3 27.6 1.0
C3B N:HEA516 4.3 21.5 1.0
C2B N:HEA516 4.3 22.8 1.0
CG N:HIS376 4.3 25.5 1.0
C2A N:HEA516 4.4 20.6 1.0
C3C N:HEA516 4.4 22.8 1.0
C2C N:HEA516 4.4 20.6 1.0
C3A N:HEA516 4.4 19.4 1.0
CG2 N:VAL380 4.8 31.1 1.0

Reference:

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa. A Histidine Residue Acting As A Controlling Site For Dioxygen Reduction and Proton Pumping By Cytochrome C Oxidase Proc.Natl.Acad.Sci.Usa V. 104 7881 2007.
ISSN: ISSN 0027-8424
PubMed: 17470809
DOI: 10.1073/PNAS.0610031104
Page generated: Thu Jul 17 00:54:01 2025

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