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Iron in PDB 3asn: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength, PDB code: 3asn 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 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.826, 204.098, 177.829, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.7

Other elements in 3asn:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength (pdb code 3asn). 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 1.7470 Angstrom Wavelength, PDB code: 3asn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3asn

Go back to Iron Binding Sites List in 3asn
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 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 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:25.6
occ:1.00
 FE A:HEA515 0.0 25.6 1.0
NE2 A:HIS378 2.0 18.8 1.0
NE2 A:HIS61 2.1 18.6 1.0
NC A:HEA515 2.1 19.5 1.0
NB A:HEA515 2.1 18.9 1.0
ND A:HEA515 2.1 18.2 1.0
NA A:HEA515 2.1 18.5 1.0
CE1 A:HIS378 2.8 16.6 1.0
CD2 A:HIS378 3.0 16.2 1.0
CE1 A:HIS61 3.0 14.3 1.0
C4C A:HEA515 3.0 19.9 1.0
CD2 A:HIS61 3.0 14.4 1.0
C1B A:HEA515 3.1 18.7 1.0
C1C A:HEA515 3.1 19.9 1.0
C1D A:HEA515 3.1 16.2 1.0
C4B A:HEA515 3.1 18.8 1.0
C4A A:HEA515 3.1 17.5 1.0
C4D A:HEA515 3.1 19.1 1.0
C1A A:HEA515 3.1 19.5 1.0
CHB A:HEA515 3.4 18.6 1.0
CHD A:HEA515 3.4 16.6 1.0
CHC A:HEA515 3.5 18.9 1.0
CHA A:HEA515 3.5 18.2 1.0
ND1 A:HIS378 4.0 18.5 1.0
CG A:HIS378 4.1 17.2 1.0
ND1 A:HIS61 4.1 14.1 1.0
CG A:HIS61 4.2 14.8 1.0
C2B A:HEA515 4.2 16.9 1.0
C3C A:HEA515 4.3 21.6 1.0
C2C A:HEA515 4.3 20.1 1.0
C3B A:HEA515 4.3 16.6 1.0
C2D A:HEA515 4.3 16.0 1.0
C3A A:HEA515 4.3 17.4 1.0
C3D A:HEA515 4.3 18.8 1.0
C2A A:HEA515 4.4 19.0 1.0
CE2 A:PHE377 4.8 10.9 1.0

Iron binding site 2 out of 4 in 3asn

Go back to Iron Binding Sites List in 3asn
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 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 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:26.8
occ:1.00
 FE A:HEA516 0.0 26.8 1.0
NA A:HEA516 2.1 17.3 1.0
NB A:HEA516 2.1 18.6 1.0
NC A:HEA516 2.1 16.6 1.0
ND A:HEA516 2.1 17.6 1.0
NE2 A:HIS376 2.3 20.7 1.0
C1A A:HEA516 3.0 15.7 1.0
C4A A:HEA516 3.1 15.8 1.0
C1B A:HEA516 3.1 17.2 1.0
C1C A:HEA516 3.1 18.0 1.0
C4B A:HEA516 3.1 18.4 1.0
C4D A:HEA516 3.1 13.7 1.0
C1D A:HEA516 3.1 15.1 1.0
C4C A:HEA516 3.1 14.1 1.0
CE1 A:HIS376 3.1 18.1 1.0
CD2 A:HIS376 3.4 18.6 1.0
CHB A:HEA516 3.4 18.1 1.0
CHA A:HEA516 3.4 13.8 1.0
CHC A:HEA516 3.5 17.5 1.0
CHD A:HEA516 3.5 10.5 1.0
C2A A:HEA516 4.3 15.1 1.0
C3A A:HEA516 4.3 14.9 1.0
C2B A:HEA516 4.3 15.6 1.0
C3B A:HEA516 4.3 16.8 1.0
C2D A:HEA516 4.3 14.2 1.0
C3D A:HEA516 4.3 13.0 1.0
ND1 A:HIS376 4.3 17.8 1.0
C2C A:HEA516 4.3 16.8 1.0
C3C A:HEA516 4.3 16.3 1.0
CG A:HIS376 4.4 17.4 1.0
CU A:CU517 4.7 22.5 1.0

Iron binding site 3 out of 4 in 3asn

Go back to Iron Binding Sites List in 3asn
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 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 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:41.8
occ:1.00
 FE N:HEA515 0.0 41.8 1.0
NE2 N:HIS378 2.0 18.8 1.0
NB N:HEA515 2.0 55.1 1.0
NE2 N:HIS61 2.0 21.5 1.0
NA N:HEA515 2.1 69.8 1.0
ND N:HEA515 2.1 59.3 1.0
NC N:HEA515 2.1 57.3 1.0
CE1 N:HIS378 2.9 16.5 1.0
C1B N:HEA515 3.0 39.5 1.0
CE1 N:HIS61 3.0 16.3 1.0
C4B N:HEA515 3.0 35.9 1.0
CD2 N:HIS61 3.0 17.9 1.0
C4A N:HEA515 3.0 64.4 1.0
C1A N:HEA515 3.0 62.7 1.0
C1D N:HEA515 3.1 46.6 1.0
C4C N:HEA515 3.1 38.4 1.0
CD2 N:HIS378 3.1 15.4 1.0
C4D N:HEA515 3.1 56.4 1.0
C1C N:HEA515 3.1 57.2 1.0
CHB N:HEA515 3.4 69.2 1.0
CHA N:HEA515 3.4 53.1 1.0
CHC N:HEA515 3.4 42.5 1.0
CHD N:HEA515 3.4 40.8 1.0
ND1 N:HIS378 4.0 17.2 1.0
ND1 N:HIS61 4.1 16.9 1.0
CG N:HIS61 4.2 19.1 1.0
CG N:HIS378 4.2 18.2 1.0
C2B N:HEA515 4.2 36.4 1.0
C3A N:HEA515 4.2 70.3 1.0
C2A N:HEA515 4.2 66.0 1.0
C3B N:HEA515 4.3 39.5 1.0
C2D N:HEA515 4.3 33.8 1.0
C3C N:HEA515 4.3 43.2 1.0
C2C N:HEA515 4.3 40.2 1.0
C3D N:HEA515 4.3 35.4 1.0
CE2 N:PHE377 4.8 14.3 1.0

Iron binding site 4 out of 4 in 3asn

Go back to Iron Binding Sites List in 3asn
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 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 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:21.9
occ:1.00
 FE N:HEA516 0.0 21.9 1.0
ND N:HEA516 2.1 21.5 1.0
NB N:HEA516 2.1 15.9 1.0
NA N:HEA516 2.1 20.1 1.0
NC N:HEA516 2.1 20.6 1.0
NE2 N:HIS376 2.3 21.8 1.0
C1D N:HEA516 3.0 19.7 1.0
C4D N:HEA516 3.1 19.5 1.0
C1B N:HEA516 3.1 15.7 1.0
C4A N:HEA516 3.1 17.5 1.0
C4B N:HEA516 3.1 15.6 1.0
C4C N:HEA516 3.1 17.5 1.0
C1A N:HEA516 3.1 19.3 1.0
C1C N:HEA516 3.1 18.6 1.0
CD2 N:HIS376 3.2 20.5 1.0
CE1 N:HIS376 3.3 20.4 1.0
CHB N:HEA516 3.4 18.9 1.0
CHA N:HEA516 3.4 15.7 1.0
CHD N:HEA516 3.5 17.6 1.0
CHC N:HEA516 3.5 18.5 1.0
C2D N:HEA516 4.2 17.3 1.0
C3D N:HEA516 4.3 17.5 1.0
C3B N:HEA516 4.3 14.5 1.0
C2B N:HEA516 4.3 11.8 1.0
C3A N:HEA516 4.3 17.7 1.0
C2C N:HEA516 4.3 16.9 1.0
C3C N:HEA516 4.3 19.1 1.0
C2A N:HEA516 4.3 16.0 1.0
CG N:HIS376 4.4 18.8 1.0
ND1 N:HIS376 4.4 17.5 1.0
CU N:CU517 4.7 24.9 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 Dec 13 15:01:13 2020

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