Atomistry » Iron » PDB 2e1s-2eus » 2eik
Atomistry »
  Iron »
    PDB 2e1s-2eus »
      2eik »

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: Sat Aug 3 21:07:29 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy