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Iron in PDB 2ein: Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

Enzymatic activity of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

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

Protein crystallography data

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2ein 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 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 187.810, 203.581, 177.927, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.8

Other elements in 2ein:

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

Magnesium (Mg) 2 atoms
Zinc (Zn) 14 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 2ein

Go back to Iron Binding Sites List in 2ein
Iron binding site 1 out of 4 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the 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 Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:31.2
occ:1.00
 FE A:HEA515 0.0 31.2 1.0
NE2 A:HIS61 1.8 18.5 1.0
NA A:HEA515 1.9 51.9 1.0
NB A:HEA515 1.9 44.0 1.0
ND A:HEA515 1.9 43.4 1.0
NE2 A:HIS378 1.9 13.4 1.0
NC A:HEA515 2.0 50.4 1.0
CE1 A:HIS378 2.8 20.5 1.0
CD2 A:HIS61 2.8 22.6 1.0
CE1 A:HIS61 2.8 21.1 1.0
C1B A:HEA515 2.9 51.4 1.0
C4A A:HEA515 2.9 53.1 1.0
C1D A:HEA515 3.0 47.3 1.0
C4D A:HEA515 3.0 47.7 1.0
C4B A:HEA515 3.0 46.2 1.0
C1A A:HEA515 3.0 50.6 1.0
C4C A:HEA515 3.0 50.5 1.0
C1C A:HEA515 3.0 49.4 1.0
CD2 A:HIS378 3.1 24.8 1.0
CHB A:HEA515 3.2 55.3 1.0
CHD A:HEA515 3.3 50.3 1.0
CHA A:HEA515 3.4 50.4 1.0
CHC A:HEA515 3.4 50.0 1.0
ND1 A:HIS61 3.9 23.3 1.0
CG A:HIS61 4.0 24.1 1.0
ND1 A:HIS378 4.0 23.2 1.0
C3A A:HEA515 4.1 53.2 1.0
CG A:HIS378 4.2 24.5 1.0
C2B A:HEA515 4.2 54.9 1.0
C2A A:HEA515 4.2 52.3 1.0
C3D A:HEA515 4.2 47.1 1.0
C2D A:HEA515 4.2 42.2 1.0
C3B A:HEA515 4.2 50.8 1.0
C3C A:HEA515 4.2 52.8 1.0
C2C A:HEA515 4.3 52.6 1.0
CE2 A:PHE377 4.6 39.4 1.0

Iron binding site 2 out of 4 in 2ein

Go back to Iron Binding Sites List in 2ein
Iron binding site 2 out of 4 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the 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 Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:34.0
occ:1.00
 FE A:HEA516 0.0 34.0 1.0
ND A:HEA516 1.8 41.8 1.0
NB A:HEA516 1.9 40.3 1.0
NA A:HEA516 1.9 50.4 1.0
NC A:HEA516 2.0 49.5 1.0
NE2 A:HIS376 2.1 23.4 1.0
CE1 A:HIS376 2.8 30.1 1.0
C1D A:HEA516 2.8 39.9 1.0
C4D A:HEA516 2.9 43.9 1.0
C1B A:HEA516 2.9 37.8 1.0
C4B A:HEA516 2.9 41.7 1.0
C4A A:HEA516 3.0 48.6 1.0
C1A A:HEA516 3.0 45.4 1.0
C4C A:HEA516 3.0 45.7 1.0
C1C A:HEA516 3.0 47.1 1.0
CHB A:HEA516 3.3 46.6 1.0
CD2 A:HIS376 3.3 30.6 1.0
CHA A:HEA516 3.3 45.6 1.0
CHD A:HEA516 3.3 46.9 1.0
CHC A:HEA516 3.4 41.9 1.0
C2D A:HEA516 4.1 41.8 1.0
ND1 A:HIS376 4.1 29.0 1.0
C3D A:HEA516 4.1 42.6 1.0
C2B A:HEA516 4.1 39.2 1.0
C3B A:HEA516 4.1 43.0 1.0
C2A A:HEA516 4.2 41.3 1.0
C3A A:HEA516 4.2 43.7 1.0
C2C A:HEA516 4.3 48.4 1.0
C3C A:HEA516 4.3 46.4 1.0
CG A:HIS376 4.3 29.3 1.0
CU A:CU517 4.6 41.4 1.0
CG2 A:VAL243 5.0 31.4 1.0

Iron binding site 3 out of 4 in 2ein

Go back to Iron Binding Sites List in 2ein
Iron binding site 3 out of 4 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the 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 Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:46.2
occ:1.00
 FE N:HEA515 0.0 46.2 1.0
NA N:HEA515 1.8 53.9 1.0
ND N:HEA515 1.9 50.5 1.0
NE2 N:HIS378 1.9 36.4 1.0
NB N:HEA515 2.0 46.1 1.0
NE2 N:HIS61 2.0 36.4 1.0
NC N:HEA515 2.0 54.4 1.0
CE1 N:HIS378 2.8 33.4 1.0
CD2 N:HIS61 2.8 30.3 1.0
C4A N:HEA515 2.9 53.3 1.0
C1A N:HEA515 2.9 58.2 1.0
C4D N:HEA515 2.9 55.2 1.0
C1D N:HEA515 2.9 56.1 1.0
C1B N:HEA515 2.9 50.1 1.0
C4C N:HEA515 3.0 54.1 1.0
C4B N:HEA515 3.0 42.2 1.0
C1C N:HEA515 3.1 51.2 1.0
CD2 N:HIS378 3.1 36.9 1.0
CE1 N:HIS61 3.1 36.6 1.0
CHB N:HEA515 3.3 50.2 1.0
CHA N:HEA515 3.3 58.3 1.0
CHD N:HEA515 3.4 54.2 1.0
CHC N:HEA515 3.4 48.4 1.0
ND1 N:HIS378 4.0 32.6 1.0
CG N:HIS61 4.0 34.5 1.0
C3A N:HEA515 4.1 59.3 1.0
CG N:HIS378 4.1 41.1 1.0
C2A N:HEA515 4.1 59.6 1.0
ND1 N:HIS61 4.2 35.9 1.0
C3D N:HEA515 4.2 56.0 1.0
C2B N:HEA515 4.2 49.5 1.0
C2D N:HEA515 4.2 55.3 1.0
C3B N:HEA515 4.2 45.0 1.0
C3C N:HEA515 4.2 53.5 1.0
C2C N:HEA515 4.3 52.2 1.0
CE2 N:PHE377 5.0 53.0 1.0

Iron binding site 4 out of 4 in 2ein

Go back to Iron Binding Sites List in 2ein
Iron binding site 4 out of 4 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the 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 Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:43.6
occ:1.00
 FE N:HEA516 0.0 43.6 1.0
ND N:HEA516 1.7 43.7 1.0
NA N:HEA516 1.9 49.4 1.0
NB N:HEA516 1.9 44.1 1.0
NC N:HEA516 2.0 50.2 1.0
NE2 N:HIS376 2.2 39.0 1.0
C4D N:HEA516 2.8 42.7 1.0
C1D N:HEA516 2.8 44.4 1.0
C1A N:HEA516 2.9 49.3 1.0
C1B N:HEA516 2.9 40.4 1.0
C4A N:HEA516 3.0 50.1 1.0
CE1 N:HIS376 3.0 44.1 1.0
C4B N:HEA516 3.0 43.6 1.0
C4C N:HEA516 3.0 47.5 1.0
C1C N:HEA516 3.1 47.9 1.0
CHA N:HEA516 3.3 42.3 1.0
CHB N:HEA516 3.3 50.3 1.0
CHD N:HEA516 3.3 46.5 1.0
CD2 N:HIS376 3.4 46.5 1.0
CHC N:HEA516 3.5 40.3 1.0
C3D N:HEA516 4.0 42.6 1.0
C2D N:HEA516 4.0 40.5 1.0
C2B N:HEA516 4.2 35.1 1.0
C2A N:HEA516 4.2 50.3 1.0
C3B N:HEA516 4.2 40.3 1.0
C3A N:HEA516 4.2 49.8 1.0
ND1 N:HIS376 4.3 44.9 1.0
C2C N:HEA516 4.3 49.2 1.0
C3C N:HEA516 4.3 46.8 1.0
CU N:CU517 4.3 48.3 1.0
CG N:HIS376 4.5 47.0 1.0
CE1 N:HIS240 4.9 46.6 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 21:07:49 2024

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