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

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

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

Protein crystallography data

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eim 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 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.909, 206.721, 178.337, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.6

Other elements in 2eim:

The structure of Zinc 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) 6 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 Reduced State (pdb code 2eim). 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 Reduced State, PDB code: 2eim:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2eim

Go back to Iron Binding Sites List in 2eim
Iron binding site 1 out of 4 in the Zinc 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 Zinc 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:17.7
occ:1.00
 FE A:HEA515 0.0 17.7 1.0
NE2 A:HIS378 1.8 15.1 1.0
NB A:HEA515 1.9 17.9 1.0
NA A:HEA515 2.0 31.4 1.0
NC A:HEA515 2.0 25.0 1.0
ND A:HEA515 2.0 20.9 1.0
NE2 A:HIS61 2.1 23.1 1.0
CE1 A:HIS378 2.7 22.9 1.0
C1B A:HEA515 2.9 18.7 1.0
C4C A:HEA515 3.0 24.7 1.0
C1D A:HEA515 3.0 16.6 1.0
C4A A:HEA515 3.0 29.6 1.0
C4B A:HEA515 3.0 22.0 1.0
C4D A:HEA515 3.0 27.5 1.0
C1A A:HEA515 3.0 28.9 1.0
CD2 A:HIS378 3.0 23.4 1.0
CD2 A:HIS61 3.1 27.8 1.0
CE1 A:HIS61 3.1 29.4 1.0
C1C A:HEA515 3.1 17.4 1.0
CHD A:HEA515 3.3 18.6 1.0
CHB A:HEA515 3.3 23.0 1.0
CHA A:HEA515 3.5 26.5 1.0
CHC A:HEA515 3.5 16.1 1.0
ND1 A:HIS378 3.9 21.9 1.0
CG A:HIS378 4.1 20.3 1.0
C3B A:HEA515 4.2 21.8 1.0
C2B A:HEA515 4.2 19.6 1.0
C2D A:HEA515 4.2 23.0 1.0
C2A A:HEA515 4.2 31.2 1.0
C3A A:HEA515 4.2 30.8 1.0
ND1 A:HIS61 4.2 27.3 1.0
C3C A:HEA515 4.2 22.6 1.0
CG A:HIS61 4.2 23.9 1.0
C3D A:HEA515 4.2 27.2 1.0
C2C A:HEA515 4.3 24.8 1.0
OG A:SER382 4.5 55.2 1.0
CE2 A:PHE377 4.8 21.9 1.0

Iron binding site 2 out of 4 in 2eim

Go back to Iron Binding Sites List in 2eim
Iron binding site 2 out of 4 in the Zinc 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 Zinc 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:28.1
occ:1.00
 FE A:HEA516 0.0 28.1 1.0
NB A:HEA516 1.8 40.4 1.0
NA A:HEA516 1.9 47.5 1.0
NE2 A:HIS376 2.0 16.2 1.0
ND A:HEA516 2.0 41.5 1.0
NC A:HEA516 2.2 44.5 1.0
CE1 A:HIS376 2.7 22.1 1.0
C1B A:HEA516 2.9 43.3 1.0
C4B A:HEA516 2.9 44.3 1.0
C4A A:HEA516 3.0 47.8 1.0
C1A A:HEA516 3.0 39.9 1.0
C4D A:HEA516 3.1 39.9 1.0
C1D A:HEA516 3.1 38.1 1.0
C1C A:HEA516 3.2 43.2 1.0
C4C A:HEA516 3.2 39.9 1.0
CD2 A:HIS376 3.2 18.9 1.0
CHB A:HEA516 3.3 50.3 1.0
CHA A:HEA516 3.4 43.7 1.0
CHC A:HEA516 3.4 45.0 1.0
CHD A:HEA516 3.5 35.6 1.0
ND1 A:HIS376 3.9 17.3 1.0
C2B A:HEA516 4.1 43.4 1.0
C3B A:HEA516 4.1 44.1 1.0
CG A:HIS376 4.2 15.5 1.0
C3A A:HEA516 4.2 43.0 1.0
C2A A:HEA516 4.2 41.9 1.0
C3D A:HEA516 4.3 36.0 1.0
C2D A:HEA516 4.3 35.7 1.0
C2C A:HEA516 4.4 46.0 1.0
C3C A:HEA516 4.5 46.9 1.0
CG2 A:VAL380 5.0 25.1 1.0

Iron binding site 3 out of 4 in 2eim

Go back to Iron Binding Sites List in 2eim
Iron binding site 3 out of 4 in the Zinc 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 Zinc 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:32.4
occ:1.00
 FE N:HEA515 0.0 32.4 1.0
NC N:HEA515 1.9 26.8 1.0
ND N:HEA515 1.9 22.4 1.0
NB N:HEA515 1.9 23.4 1.0
NA N:HEA515 1.9 26.0 1.0
NE2 N:HIS61 2.0 42.2 1.0
NE2 N:HIS378 2.0 28.4 1.0
CE1 N:HIS378 2.8 29.5 1.0
C4C N:HEA515 2.9 30.4 1.0
CD2 N:HIS61 2.9 38.1 1.0
C1D N:HEA515 2.9 20.5 1.0
C4D N:HEA515 3.0 27.2 1.0
C1B N:HEA515 3.0 26.6 1.0
C1A N:HEA515 3.0 29.6 1.0
C4A N:HEA515 3.0 29.1 1.0
C4B N:HEA515 3.0 30.4 1.0
C1C N:HEA515 3.0 28.1 1.0
CE1 N:HIS61 3.1 44.2 1.0
CD2 N:HIS378 3.3 31.1 1.0
CHD N:HEA515 3.3 22.0 1.0
CHB N:HEA515 3.4 24.8 1.0
CHA N:HEA515 3.4 28.5 1.0
CHC N:HEA515 3.5 21.3 1.0
ND1 N:HIS378 4.1 28.6 1.0
CG N:HIS61 4.1 39.4 1.0
C2D N:HEA515 4.1 25.1 1.0
C3C N:HEA515 4.2 28.6 1.0
C3D N:HEA515 4.2 27.4 1.0
C2A N:HEA515 4.2 29.2 1.0
C3B N:HEA515 4.2 33.9 1.0
ND1 N:HIS61 4.2 37.2 1.0
C2B N:HEA515 4.2 27.2 1.0
C3A N:HEA515 4.2 28.8 1.0
C2C N:HEA515 4.3 31.1 1.0
CG N:HIS378 4.3 26.3 1.0
OG N:SER382 4.5 58.0 1.0
CE2 N:PHE377 4.6 30.0 1.0

Iron binding site 4 out of 4 in 2eim

Go back to Iron Binding Sites List in 2eim
Iron binding site 4 out of 4 in the Zinc 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 Zinc 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:36.8
occ:1.00
 FE N:HEA516 0.0 36.8 1.0
NB N:HEA516 1.8 45.9 1.0
NA N:HEA516 1.9 46.0 1.0
ND N:HEA516 2.0 42.5 1.0
NE2 N:HIS376 2.0 28.2 1.0
NC N:HEA516 2.1 43.6 1.0
C1B N:HEA516 2.9 44.0 1.0
C4B N:HEA516 2.9 45.0 1.0
C4A N:HEA516 2.9 46.6 1.0
CE1 N:HIS376 2.9 34.6 1.0
C1A N:HEA516 3.0 46.6 1.0
C4D N:HEA516 3.1 42.1 1.0
C1D N:HEA516 3.1 44.8 1.0
CD2 N:HIS376 3.1 27.1 1.0
C1C N:HEA516 3.1 43.5 1.0
C4C N:HEA516 3.2 46.4 1.0
CHB N:HEA516 3.3 43.9 1.0
CHA N:HEA516 3.4 46.8 1.0
CHC N:HEA516 3.4 44.9 1.0
CHD N:HEA516 3.5 50.1 1.0
C2B N:HEA516 4.1 45.3 1.0
C3B N:HEA516 4.1 44.4 1.0
ND1 N:HIS376 4.1 36.5 1.0
CG N:HIS376 4.2 18.4 1.0
C3A N:HEA516 4.2 48.4 1.0
C2A N:HEA516 4.2 46.5 1.0
C3D N:HEA516 4.3 40.3 1.0
C2D N:HEA516 4.3 40.3 1.0
C2C N:HEA516 4.4 44.6 1.0
C3C N:HEA516 4.4 46.1 1.0
CG2 N:VAL380 4.9 32.2 1.0
CU N:CU517 5.0 36.1 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 21:07:45 2024

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