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Iron in PDB 3abm: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset), PDB code: 3abm was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.697, 206.991, 178.251, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.4

Other elements in 3abm:

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset) also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset) (pdb code 3abm). 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 at the Fully Oxidized State (200-S X-Ray Exposure Dataset), PDB code: 3abm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3abm

Go back to Iron Binding Sites List in 3abm
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)


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 at the Fully Oxidized State (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:25.7
occ:1.00
FE A:HEA515 0.0 25.7 1.0
NE2 A:HIS61 1.9 20.1 1.0
NB A:HEA515 1.9 22.3 1.0
NE2 A:HIS378 1.9 21.1 1.0
ND A:HEA515 2.0 25.3 1.0
NA A:HEA515 2.1 25.9 1.0
NC A:HEA515 2.1 23.5 1.0
CE1 A:HIS61 2.8 24.6 1.0
CE1 A:HIS378 2.9 24.9 1.0
C4B A:HEA515 2.9 25.5 1.0
CD2 A:HIS61 3.0 31.1 1.0
CD2 A:HIS378 3.0 27.4 1.0
C4D A:HEA515 3.1 21.4 1.0
C4A A:HEA515 3.1 26.5 1.0
C1D A:HEA515 3.1 26.3 1.0
C1B A:HEA515 3.1 31.0 1.0
C4C A:HEA515 3.1 28.2 1.0
C1A A:HEA515 3.1 25.0 1.0
C1C A:HEA515 3.1 25.5 1.0
CHC A:HEA515 3.4 20.2 1.0
CHD A:HEA515 3.4 24.6 1.0
CHB A:HEA515 3.5 26.6 1.0
CHA A:HEA515 3.5 24.5 1.0
ND1 A:HIS61 4.0 24.6 1.0
ND1 A:HIS378 4.0 26.9 1.0
CG A:HIS61 4.1 23.1 1.0
CG A:HIS378 4.1 22.8 1.0
C3B A:HEA515 4.2 21.6 1.0
C3A A:HEA515 4.3 21.0 1.0
C2B A:HEA515 4.3 19.6 1.0
C2A A:HEA515 4.3 28.1 1.0
C2D A:HEA515 4.3 24.4 1.0
C3D A:HEA515 4.3 25.3 1.0
C2C A:HEA515 4.3 22.7 1.0
C3C A:HEA515 4.4 23.6 1.0
CE2 A:PHE377 4.9 28.2 1.0

Iron binding site 2 out of 4 in 3abm

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Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)


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 at the Fully Oxidized State (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:27.1
occ:1.00
FE A:HEA516 0.0 27.1 1.0
ND A:HEA516 2.0 26.8 1.0
NA A:HEA516 2.0 22.3 1.0
NE2 A:HIS376 2.0 21.5 1.0
NB A:HEA516 2.0 29.8 1.0
NC A:HEA516 2.1 29.3 1.0
O1 A:PER520 2.2 25.6 1.0
CE1 A:HIS376 2.9 30.1 1.0
C1A A:HEA516 3.0 23.8 1.0
C4D A:HEA516 3.0 32.1 1.0
C4A A:HEA516 3.0 20.9 1.0
C4B A:HEA516 3.1 31.2 1.0
C1B A:HEA516 3.1 29.4 1.0
C1C A:HEA516 3.1 26.2 1.0
CD2 A:HIS376 3.1 30.6 1.0
C1D A:HEA516 3.1 30.6 1.0
C4C A:HEA516 3.1 20.3 1.0
CHA A:HEA516 3.4 23.4 1.0
CHC A:HEA516 3.5 26.4 1.0
CHB A:HEA516 3.5 24.1 1.0
CHD A:HEA516 3.6 22.5 1.0
O2 A:PER520 3.6 32.9 1.0
ND1 A:HIS376 4.1 28.4 1.0
C3A A:HEA516 4.2 22.4 1.0
C2A A:HEA516 4.2 21.2 1.0
CG A:HIS376 4.2 25.1 1.0
C3D A:HEA516 4.2 25.4 1.0
C2D A:HEA516 4.3 25.3 1.0
C2C A:HEA516 4.3 27.2 1.0
C3B A:HEA516 4.3 26.4 1.0
C2B A:HEA516 4.3 22.7 1.0
C3C A:HEA516 4.3 26.6 1.0
CU A:CU517 4.9 29.1 1.0

Iron binding site 3 out of 4 in 3abm

Go back to Iron Binding Sites List in 3abm
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)


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 at the Fully Oxidized State (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:31.1
occ:1.00
FE N:HEA515 0.0 31.1 1.0
NE2 N:HIS378 2.0 27.6 1.0
ND N:HEA515 2.0 27.7 1.0
NB N:HEA515 2.0 29.7 1.0
NE2 N:HIS61 2.0 26.8 1.0
NC N:HEA515 2.1 31.5 1.0
NA N:HEA515 2.2 28.9 1.0
CE1 N:HIS378 2.9 30.1 1.0
CD2 N:HIS61 2.9 32.5 1.0
CD2 N:HIS378 3.0 29.2 1.0
C4D N:HEA515 3.0 28.5 1.0
C4B N:HEA515 3.0 34.5 1.0
C1D N:HEA515 3.0 35.2 1.0
CE1 N:HIS61 3.0 31.3 1.0
C1B N:HEA515 3.1 37.9 1.0
C4C N:HEA515 3.1 33.7 1.0
C4A N:HEA515 3.1 28.4 1.0
C1A N:HEA515 3.2 28.4 1.0
C1C N:HEA515 3.2 31.4 1.0
CHD N:HEA515 3.4 31.9 1.0
CHC N:HEA515 3.5 30.9 1.0
CHA N:HEA515 3.5 28.4 1.0
CHB N:HEA515 3.5 34.8 1.0
ND1 N:HIS378 4.1 29.0 1.0
CG N:HIS61 4.1 30.9 1.0
CG N:HIS378 4.1 30.8 1.0
ND1 N:HIS61 4.1 27.5 1.0
C3D N:HEA515 4.2 23.1 1.0
C3B N:HEA515 4.3 32.6 1.0
C2B N:HEA515 4.3 34.8 1.0
C2D N:HEA515 4.3 30.8 1.0
C3C N:HEA515 4.3 30.6 1.0
C2A N:HEA515 4.3 30.8 1.0
C3A N:HEA515 4.3 27.4 1.0
C2C N:HEA515 4.4 26.4 1.0
CE2 N:PHE377 4.8 34.1 1.0

Iron binding site 4 out of 4 in 3abm

Go back to Iron Binding Sites List in 3abm
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)


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 at the Fully Oxidized State (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:33.7
occ:1.00
FE N:HEA516 0.0 33.7 1.0
ND N:HEA516 2.0 33.8 1.0
NE2 N:HIS376 2.0 34.6 1.0
NC N:HEA516 2.1 33.8 1.0
NB N:HEA516 2.1 36.5 1.0
NA N:HEA516 2.1 31.2 1.0
O1 N:PER520 2.4 31.0 1.0
CE1 N:HIS376 3.0 39.7 1.0
C1B N:HEA516 3.0 35.6 1.0
C4D N:HEA516 3.0 35.1 1.0
C1D N:HEA516 3.0 34.4 1.0
C1C N:HEA516 3.1 33.0 1.0
CD2 N:HIS376 3.1 35.2 1.0
C1A N:HEA516 3.1 28.9 1.0
C4C N:HEA516 3.1 31.0 1.0
C4B N:HEA516 3.1 34.0 1.0
C4A N:HEA516 3.1 28.3 1.0
CHB N:HEA516 3.4 30.4 1.0
CHC N:HEA516 3.5 33.6 1.0
CHA N:HEA516 3.5 30.2 1.0
CHD N:HEA516 3.6 30.1 1.0
O2 N:PER520 3.8 35.0 1.0
ND1 N:HIS376 4.1 34.0 1.0
CG N:HIS376 4.2 32.6 1.0
C2D N:HEA516 4.2 31.4 1.0
C2B N:HEA516 4.3 32.4 1.0
C3D N:HEA516 4.3 32.5 1.0
C2C N:HEA516 4.3 29.2 1.0
C3A N:HEA516 4.3 26.4 1.0
C3B N:HEA516 4.3 30.1 1.0
C3C N:HEA516 4.3 32.2 1.0
C2A N:HEA516 4.4 27.6 1.0
CU N:CU517 4.9 32.4 1.0

Reference:

H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa. A Peroxide Bridge Between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump Proc.Natl.Acad.Sci.Usa V. 106 2165 2009.
ISSN: ISSN 0027-8424
PubMed: 19164527
DOI: 10.1073/PNAS.0806391106
Page generated: Sun Dec 13 15:00:13 2020

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