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Iron in PDB 2zxw: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-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 (1-S X- Ray Exposure Dataset), PDB code: 2zxw was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, 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 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 184.156, 207.621, 178.247, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.3

Other elements in 2zxw:

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

Iron binding site 1 out of 4 in 2zxw

Go back to Iron Binding Sites List in 2zxw
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-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 (1-S X- Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:14.8
occ:1.00
 FE A:HEA515 0.0 14.8 1.0
NE2 A:HIS378 1.9 16.2 1.0
NE2 A:HIS61 2.0 11.9 1.0
ND A:HEA515 2.0 16.7 1.0
NC A:HEA515 2.0 17.8 1.0
NB A:HEA515 2.1 17.9 1.0
NA A:HEA515 2.2 18.1 1.0
CE1 A:HIS378 2.8 13.0 1.0
CE1 A:HIS61 2.9 14.2 1.0
CD2 A:HIS61 3.0 10.9 1.0
C1D A:HEA515 3.0 17.6 1.0
CD2 A:HIS378 3.0 14.4 1.0
C4C A:HEA515 3.0 17.9 1.0
C1C A:HEA515 3.0 16.5 1.0
C4D A:HEA515 3.0 16.5 1.0
C1B A:HEA515 3.1 17.9 1.0
C1A A:HEA515 3.1 19.0 1.0
C4A A:HEA515 3.1 15.4 1.0
C4B A:HEA515 3.1 17.9 1.0
CHD A:HEA515 3.4 17.5 1.0
CHB A:HEA515 3.4 16.5 1.0
CHC A:HEA515 3.5 16.5 1.0
CHA A:HEA515 3.5 15.4 1.0
ND1 A:HIS378 3.9 11.2 1.0
ND1 A:HIS61 4.0 12.1 1.0
CG A:HIS378 4.1 13.3 1.0
CG A:HIS61 4.1 10.2 1.0
C2D A:HEA515 4.2 13.7 1.0
C2C A:HEA515 4.2 21.9 1.0
C3D A:HEA515 4.2 13.1 1.0
C3C A:HEA515 4.2 18.4 1.0
C3A A:HEA515 4.3 18.2 1.0
C2B A:HEA515 4.3 16.7 1.0
C2A A:HEA515 4.3 19.5 1.0
C3B A:HEA515 4.4 15.6 1.0
CE2 A:PHE377 4.7 22.6 1.0

Iron binding site 2 out of 4 in 2zxw

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Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-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 (1-S X- Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:15.0
occ:1.00
 FE A:HEA516 0.0 15.0 1.0
NB A:HEA516 2.0 16.4 1.0
NA A:HEA516 2.1 17.1 1.0
NE2 A:HIS376 2.1 13.0 1.0
NC A:HEA516 2.2 18.9 1.0
ND A:HEA516 2.2 19.6 1.0
O1 A:PER520 2.2 8.5 1.0
CE1 A:HIS376 2.9 13.4 1.0
C4B A:HEA516 3.0 18.7 1.0
C4A A:HEA516 3.0 16.5 1.0
C1B A:HEA516 3.1 16.4 1.0
C4C A:HEA516 3.1 18.9 1.0
C4D A:HEA516 3.2 19.1 1.0
C1C A:HEA516 3.2 19.5 1.0
C1A A:HEA516 3.2 15.0 1.0
CD2 A:HIS376 3.2 11.5 1.0
C1D A:HEA516 3.3 20.9 1.0
CHB A:HEA516 3.4 18.0 1.0
CHC A:HEA516 3.4 19.9 1.0
CHD A:HEA516 3.6 20.4 1.0
CHA A:HEA516 3.6 16.2 1.0
O2 A:PER520 3.8 10.5 1.0
ND1 A:HIS376 4.1 14.7 1.0
C3A A:HEA516 4.2 12.6 1.0
C3B A:HEA516 4.2 18.1 1.0
C2B A:HEA516 4.3 13.4 1.0
CG A:HIS376 4.3 13.9 1.0
C2A A:HEA516 4.3 14.7 1.0
C3C A:HEA516 4.4 20.8 1.0
C2C A:HEA516 4.4 19.7 1.0
C3D A:HEA516 4.4 20.1 1.0
C2D A:HEA516 4.5 20.0 1.0
CU A:CU517 4.9 17.2 1.0

Iron binding site 3 out of 4 in 2zxw

Go back to Iron Binding Sites List in 2zxw
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-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 (1-S X- Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:23.0
occ:1.00
 FE N:HEA515 0.0 23.0 1.0
NE2 N:HIS378 1.9 23.5 1.0
NE2 N:HIS61 2.0 25.1 1.0
NB N:HEA515 2.0 24.9 1.0
NA N:HEA515 2.1 25.1 1.0
ND N:HEA515 2.1 23.4 1.0
NC N:HEA515 2.2 25.8 1.0
CE1 N:HIS378 2.7 25.4 1.0
CD2 N:HIS61 2.9 24.1 1.0
C1B N:HEA515 3.0 25.8 1.0
C4A N:HEA515 3.0 22.8 1.0
CE1 N:HIS61 3.1 25.6 1.0
CD2 N:HIS378 3.1 24.0 1.0
C1D N:HEA515 3.1 22.9 1.0
C1A N:HEA515 3.1 23.1 1.0
C4D N:HEA515 3.1 21.9 1.0
C4B N:HEA515 3.1 26.1 1.0
C4C N:HEA515 3.1 25.0 1.0
C1C N:HEA515 3.2 27.2 1.0
CHB N:HEA515 3.4 22.8 1.0
CHA N:HEA515 3.5 20.8 1.0
CHD N:HEA515 3.5 22.7 1.0
CHC N:HEA515 3.5 24.3 1.0
ND1 N:HIS378 3.9 24.4 1.0
CG N:HIS61 4.1 23.9 1.0
CG N:HIS378 4.1 21.3 1.0
ND1 N:HIS61 4.1 21.8 1.0
C3A N:HEA515 4.2 21.6 1.0
C2B N:HEA515 4.2 25.0 1.0
C2A N:HEA515 4.3 21.3 1.0
C3B N:HEA515 4.3 26.0 1.0
C3D N:HEA515 4.3 20.1 1.0
C2D N:HEA515 4.3 22.2 1.0
C3C N:HEA515 4.4 25.5 1.0
C2C N:HEA515 4.4 26.7 1.0
CE2 N:PHE377 4.8 18.3 1.0

Iron binding site 4 out of 4 in 2zxw

Go back to Iron Binding Sites List in 2zxw
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-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 (1-S X- Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:20.4
occ:1.00
 FE N:HEA516 0.0 20.4 1.0
ND N:HEA516 2.0 21.9 1.0
NB N:HEA516 2.1 17.9 1.0
NA N:HEA516 2.2 21.4 1.0
NE2 N:HIS376 2.2 21.7 1.0
NC N:HEA516 2.2 18.9 1.0
O1 N:PER520 2.2 13.6 1.0
C4D N:HEA516 3.0 25.1 1.0
C1B N:HEA516 3.0 18.0 1.0
C1D N:HEA516 3.1 24.8 1.0
CD2 N:HIS376 3.1 22.7 1.0
C4B N:HEA516 3.1 15.9 1.0
C1A N:HEA516 3.1 21.1 1.0
C4A N:HEA516 3.1 18.5 1.0
C4C N:HEA516 3.2 21.1 1.0
C1C N:HEA516 3.2 19.2 1.0
CE1 N:HIS376 3.2 25.7 1.0
CHA N:HEA516 3.4 22.2 1.0
CHB N:HEA516 3.4 17.2 1.0
CHD N:HEA516 3.5 23.9 1.0
CHC N:HEA516 3.5 17.7 1.0
O2 N:PER520 3.6 13.6 1.0
C3D N:HEA516 4.2 26.2 1.0
CG N:HIS376 4.3 21.1 1.0
C2B N:HEA516 4.3 17.3 1.0
C2D N:HEA516 4.3 24.9 1.0
ND1 N:HIS376 4.3 25.1 1.0
C3B N:HEA516 4.3 15.7 1.0
C3A N:HEA516 4.4 19.9 1.0
C2C N:HEA516 4.4 20.1 1.0
C2A N:HEA516 4.4 17.3 1.0
C3C N:HEA516 4.4 21.6 1.0
CU N:CU517 4.8 18.6 1.0
CG2 N:VAL243 5.0 18.2 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 Aug 4 06:24:45 2024

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