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Iron in PDB 3aso: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength, PDB code: 3aso was solved by M.Suga, N.Yano, K.Muramoto, K.Shinzawa-Itoh, T.Maeda, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.874, 204.106, 177.874, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.5

Other elements in 3aso:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength (pdb code 3aso). 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 in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength, PDB code: 3aso:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3aso

Go back to Iron Binding Sites List in 3aso
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:18.2
occ:1.00
 FE A:HEA515 0.0 18.2 1.0
NE2 A:HIS378 2.0 16.9 1.0
NE2 A:HIS61 2.0 16.9 1.0
NB A:HEA515 2.0 19.1 1.0
ND A:HEA515 2.1 18.2 1.0
NC A:HEA515 2.1 19.6 1.0
NA A:HEA515 2.1 18.5 1.0
CE1 A:HIS378 2.9 17.9 1.0
CE1 A:HIS61 3.0 15.2 1.0
CD2 A:HIS61 3.0 15.4 1.0
C1B A:HEA515 3.0 20.4 1.0
C4B A:HEA515 3.1 20.9 1.0
C1D A:HEA515 3.1 20.3 1.0
C4C A:HEA515 3.1 21.0 1.0
CD2 A:HIS378 3.1 17.1 1.0
C4D A:HEA515 3.1 18.4 1.0
C1C A:HEA515 3.1 19.4 1.0
C1A A:HEA515 3.1 17.6 1.0
C4A A:HEA515 3.1 18.5 1.0
CHB A:HEA515 3.5 15.6 1.0
CHD A:HEA515 3.5 18.6 1.0
CHC A:HEA515 3.5 15.6 1.0
CHA A:HEA515 3.5 18.4 1.0
ND1 A:HIS378 4.0 19.6 1.0
ND1 A:HIS61 4.1 13.9 1.0
CG A:HIS61 4.1 16.9 1.0
CG A:HIS378 4.2 17.2 1.0
C2B A:HEA515 4.2 20.0 1.0
C3B A:HEA515 4.3 17.2 1.0
C2D A:HEA515 4.3 18.9 1.0
C3D A:HEA515 4.3 19.4 1.0
C2A A:HEA515 4.3 20.7 1.0
C3A A:HEA515 4.3 18.6 1.0
C3C A:HEA515 4.3 19.4 1.0
C2C A:HEA515 4.3 20.7 1.0
CE2 A:PHE377 4.9 17.6 1.0

Iron binding site 2 out of 4 in 3aso

Go back to Iron Binding Sites List in 3aso
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:19.8
occ:1.00
 FE A:HEA516 0.0 19.8 1.0
ND A:HEA516 2.0 17.6 1.0
NB A:HEA516 2.0 18.3 1.0
NA A:HEA516 2.1 18.1 1.0
NC A:HEA516 2.1 18.2 1.0
NE2 A:HIS376 2.2 20.4 1.0
C1D A:HEA516 3.0 18.9 1.0
C4D A:HEA516 3.0 14.1 1.0
C1A A:HEA516 3.0 15.5 1.0
CE1 A:HIS376 3.0 19.0 1.0
C1B A:HEA516 3.1 21.2 1.0
C4A A:HEA516 3.1 20.1 1.0
C1C A:HEA516 3.1 19.1 1.0
C4B A:HEA516 3.1 19.1 1.0
C4C A:HEA516 3.1 19.8 1.0
CD2 A:HIS376 3.3 19.6 1.0
CHA A:HEA516 3.4 11.6 1.0
CHB A:HEA516 3.4 20.6 1.0
CHD A:HEA516 3.5 16.4 1.0
CHC A:HEA516 3.5 15.3 1.0
C2D A:HEA516 4.2 16.7 1.0
ND1 A:HIS376 4.2 21.9 1.0
C3D A:HEA516 4.2 16.0 1.0
C3B A:HEA516 4.3 19.6 1.0
C3A A:HEA516 4.3 18.7 1.0
C2C A:HEA516 4.3 19.7 1.0
C2B A:HEA516 4.3 21.9 1.0
C2A A:HEA516 4.3 19.1 1.0
C3C A:HEA516 4.3 19.5 1.0
CG A:HIS376 4.4 19.1 1.0
CG2 A:VAL243 4.9 15.1 1.0
CU A:CU517 4.9 20.8 1.0

Iron binding site 3 out of 4 in 3aso

Go back to Iron Binding Sites List in 3aso
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:33.1
occ:1.00
 FE N:HEA515 0.0 33.1 1.0
NB N:HEA515 2.0 43.3 1.0
ND N:HEA515 2.0 39.3 1.0
NE2 N:HIS378 2.0 13.9 1.0
NE2 N:HIS61 2.0 13.1 1.0
NA N:HEA515 2.1 49.3 1.0
NC N:HEA515 2.1 50.9 1.0
CE1 N:HIS378 2.9 19.2 1.0
CE1 N:HIS61 3.0 13.8 1.0
C1D N:HEA515 3.0 34.1 1.0
CD2 N:HIS61 3.0 17.6 1.0
C1B N:HEA515 3.0 29.1 1.0
C4B N:HEA515 3.0 30.7 1.0
C1A N:HEA515 3.0 50.8 1.0
C4A N:HEA515 3.0 48.8 1.0
C4D N:HEA515 3.0 46.1 1.0
C4C N:HEA515 3.1 32.9 1.0
CD2 N:HIS378 3.1 17.6 1.0
C1C N:HEA515 3.1 45.0 1.0
CHA N:HEA515 3.4 37.5 1.0
CHB N:HEA515 3.5 44.9 1.0
CHD N:HEA515 3.5 28.8 1.0
CHC N:HEA515 3.5 30.6 1.0
ND1 N:HIS378 4.1 21.7 1.0
ND1 N:HIS61 4.1 16.7 1.0
CG N:HIS61 4.2 20.0 1.0
CG N:HIS378 4.2 19.5 1.0
C3A N:HEA515 4.2 52.6 1.0
C2A N:HEA515 4.2 45.8 1.0
C2D N:HEA515 4.2 28.0 1.0
C2B N:HEA515 4.3 30.0 1.0
C3B N:HEA515 4.3 28.1 1.0
C3C N:HEA515 4.3 33.6 1.0
C3D N:HEA515 4.3 28.2 1.0
C2C N:HEA515 4.3 30.2 1.0
CE2 N:PHE377 4.8 19.1 1.0

Iron binding site 4 out of 4 in 3aso

Go back to Iron Binding Sites List in 3aso
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:21.2
occ:1.00
 FE N:HEA516 0.0 21.2 1.0
ND N:HEA516 2.0 20.8 1.0
NB N:HEA516 2.0 17.4 1.0
NC N:HEA516 2.0 20.8 1.0
NA N:HEA516 2.1 19.0 1.0
NE2 N:HIS376 2.2 22.5 1.0
C1B N:HEA516 3.0 19.1 1.0
C1D N:HEA516 3.0 23.7 1.0
C4D N:HEA516 3.0 17.8 1.0
C4B N:HEA516 3.0 17.5 1.0
C4C N:HEA516 3.0 22.8 1.0
C1C N:HEA516 3.1 23.1 1.0
C1A N:HEA516 3.1 18.9 1.0
C4A N:HEA516 3.1 20.0 1.0
CD2 N:HIS376 3.1 19.1 1.0
CE1 N:HIS376 3.2 20.2 1.0
CHA N:HEA516 3.4 19.1 1.0
CHD N:HEA516 3.4 18.0 1.0
CHB N:HEA516 3.5 17.4 1.0
CHC N:HEA516 3.5 18.9 1.0
C2D N:HEA516 4.2 20.9 1.0
C3D N:HEA516 4.2 22.1 1.0
C2B N:HEA516 4.2 18.9 1.0
C3B N:HEA516 4.3 17.4 1.0
C2C N:HEA516 4.3 23.4 1.0
C3A N:HEA516 4.3 18.6 1.0
C3C N:HEA516 4.3 22.7 1.0
ND1 N:HIS376 4.3 20.4 1.0
CG N:HIS376 4.3 19.7 1.0
C2A N:HEA516 4.3 21.1 1.0
CU N:CU517 4.9 23.1 1.0
CG2 N:VAL243 4.9 13.4 1.0

Reference:

M.Suga, N.Yano, K.Muramoto, K.Shinzawa-Itoh, T.Maeda, E.Yamashita, T.Tsukihara, S.Yoshikawa. Distinguishing Between Cl- and O2(2-) As the Bridging Element Between FE3+ and CU2+ in Resting-Oxidized Cytochrome C Oxidase Acta Crystallogr.,Sect.D V. 67 742 2011.
ISSN: ISSN 0907-4449
PubMed: 21795816
DOI: 10.1107/S0907444911022803
Page generated: Sun Aug 4 07:24:32 2024

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