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Iron in PDB 3x2q: X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution

Enzymatic activity of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution

All present enzymatic activity of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution, PDB code: 3x2q was solved by N.Yano, K.Muramoto, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.678, 206.675, 178.201, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.4

Other elements in 3x2q:

The structure of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution 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 X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution (pdb code 3x2q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution, PDB code: 3x2q:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3x2q

Go back to Iron Binding Sites List in 3x2q
Iron binding site 1 out of 4 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:23.9
occ:1.00
FE A:HEA602 0.0 23.9 1.0
NE2 A:HIS378 1.9 22.4 1.0
NB A:HEA602 2.0 22.1 1.0
ND A:HEA602 2.0 20.9 1.0
NA A:HEA602 2.0 22.5 1.0
NC A:HEA602 2.1 22.4 1.0
NE2 A:HIS61 2.1 18.8 1.0
CE1 A:HIS378 2.9 27.0 1.0
CD2 A:HIS378 3.0 24.5 1.0
C4A A:HEA602 3.0 22.4 1.0
C1B A:HEA602 3.0 26.4 1.0
CE1 A:HIS61 3.0 21.6 1.0
C4D A:HEA602 3.0 20.2 1.0
C1A A:HEA602 3.0 23.6 1.0
C4B A:HEA602 3.0 23.1 1.0
C1D A:HEA602 3.1 22.5 1.0
C4C A:HEA602 3.1 22.1 1.0
CD2 A:HIS61 3.1 21.7 1.0
C1C A:HEA602 3.1 22.9 1.0
CHB A:HEA602 3.4 24.0 1.0
CHD A:HEA602 3.4 21.9 1.0
CHC A:HEA602 3.4 17.1 1.0
CHA A:HEA602 3.5 20.0 1.0
ND1 A:HIS378 4.0 23.2 1.0
CG A:HIS378 4.1 21.9 1.0
ND1 A:HIS61 4.2 20.3 1.0
C3A A:HEA602 4.2 21.4 1.0
C2A A:HEA602 4.2 24.2 1.0
CG A:HIS61 4.2 19.2 1.0
C3D A:HEA602 4.3 22.8 1.0
C3C A:HEA602 4.3 22.7 1.0
C2B A:HEA602 4.3 21.7 1.0
C2C A:HEA602 4.3 22.9 1.0
C2D A:HEA602 4.3 19.9 1.0
C3B A:HEA602 4.3 23.4 1.0
CE2 A:PHE377 4.9 22.6 1.0

Iron binding site 2 out of 4 in 3x2q

Go back to Iron Binding Sites List in 3x2q
Iron binding site 2 out of 4 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:24.0
occ:1.00
FE A:HEA603 0.0 24.0 1.0
NA A:HEA603 2.0 24.2 1.0
NE2 A:HIS376 2.0 18.2 1.0
NC A:HEA603 2.0 25.0 1.0
C A:CYN601 2.0 20.9 1.0
ND A:HEA603 2.1 23.1 1.0
NB A:HEA603 2.1 25.3 1.0
C4A A:HEA603 2.9 20.6 1.0
CE1 A:HIS376 2.9 25.6 1.0
C1A A:HEA603 3.0 23.9 1.0
C1C A:HEA603 3.0 21.5 1.0
C4C A:HEA603 3.0 21.6 1.0
CD2 A:HIS376 3.1 22.3 1.0
C4D A:HEA603 3.1 25.2 1.0
N A:CYN601 3.1 24.8 1.0
C1B A:HEA603 3.1 23.2 1.0
C4B A:HEA603 3.1 20.9 1.0
C1D A:HEA603 3.1 23.5 1.0
CHB A:HEA603 3.4 19.9 1.0
CHD A:HEA603 3.5 18.9 1.0
CHA A:HEA603 3.5 19.6 1.0
CHC A:HEA603 3.5 19.6 1.0
ND1 A:HIS376 4.1 22.1 1.0
C3A A:HEA603 4.2 23.2 1.0
C2A A:HEA603 4.2 23.9 1.0
CG A:HIS376 4.2 22.1 1.0
C2C A:HEA603 4.2 24.4 1.0
C3C A:HEA603 4.3 24.1 1.0
C3D A:HEA603 4.3 24.8 1.0
C2B A:HEA603 4.3 22.8 1.0
C3B A:HEA603 4.3 25.0 1.0
C2D A:HEA603 4.3 23.9 1.0
CU A:CU604 4.9 25.7 1.0
CG2 A:VAL243 5.0 24.0 1.0

Iron binding site 3 out of 4 in 3x2q

Go back to Iron Binding Sites List in 3x2q
Iron binding site 3 out of 4 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:24.7
occ:1.00
FE N:HEA602 0.0 24.7 1.0
NE2 N:HIS61 2.0 41.8 1.0
ND N:HEA602 2.0 31.6 1.0
NC N:HEA602 2.1 24.1 1.0
NA N:HEA602 2.1 46.1 1.0
NE2 N:HIS378 2.1 34.9 1.0
NB N:HEA602 2.1 18.1 1.0
CD2 N:HIS61 2.9 40.4 1.0
CE1 N:HIS378 3.0 36.5 1.0
CE1 N:HIS61 3.0 47.8 1.0
C4A N:HEA602 3.0 42.0 1.0
C1B N:HEA602 3.0 27.1 1.0
C1D N:HEA602 3.0 24.4 1.0
C4C N:HEA602 3.0 25.0 1.0
C4D N:HEA602 3.1 21.9 1.0
C1A N:HEA602 3.1 34.3 1.0
C4B N:HEA602 3.1 22.6 1.0
CD2 N:HIS378 3.1 40.3 1.0
C1C N:HEA602 3.1 24.1 1.0
CHB N:HEA602 3.4 46.6 1.0
CHD N:HEA602 3.4 15.8 1.0
CHC N:HEA602 3.5 16.8 1.0
CHA N:HEA602 3.5 21.2 1.0
CG N:HIS61 4.1 39.1 1.0
ND1 N:HIS61 4.1 39.2 1.0
ND1 N:HIS378 4.1 43.3 1.0
CG N:HIS378 4.2 44.4 1.0
C2B N:HEA602 4.2 25.5 1.0
C2A N:HEA602 4.2 41.3 1.0
C3A N:HEA602 4.2 37.6 1.0
C3B N:HEA602 4.3 22.1 1.0
C2D N:HEA602 4.3 21.7 1.0
C3D N:HEA602 4.3 15.2 1.0
C3C N:HEA602 4.3 16.8 1.0
C2C N:HEA602 4.4 25.8 1.0
CE2 N:PHE377 4.9 43.3 1.0

Iron binding site 4 out of 4 in 3x2q

Go back to Iron Binding Sites List in 3x2q
Iron binding site 4 out of 4 in the X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe603

b:30.2
occ:1.00
FE N:HEA603 0.0 30.2 1.0
C N:CYN601 1.9 31.5 1.0
NA N:HEA603 2.0 31.1 1.0
NC N:HEA603 2.0 30.9 1.0
ND N:HEA603 2.0 31.2 1.0
NE2 N:HIS376 2.1 28.8 1.0
NB N:HEA603 2.1 28.4 1.0
N N:CYN601 3.0 30.8 1.0
C1C N:HEA603 3.0 29.0 1.0
C4C N:HEA603 3.0 31.0 1.0
C4A N:HEA603 3.0 27.6 1.0
CD2 N:HIS376 3.0 30.6 1.0
C1A N:HEA603 3.0 29.5 1.0
C1D N:HEA603 3.1 29.3 1.0
C4D N:HEA603 3.1 29.9 1.0
C1B N:HEA603 3.1 32.1 1.0
C4B N:HEA603 3.1 25.2 1.0
CE1 N:HIS376 3.1 30.9 1.0
CHA N:HEA603 3.4 26.4 1.0
CHB N:HEA603 3.4 27.3 1.0
CHD N:HEA603 3.4 25.9 1.0
CHC N:HEA603 3.5 27.1 1.0
CG N:HIS376 4.2 28.5 1.0
ND1 N:HIS376 4.2 27.7 1.0
C2C N:HEA603 4.2 28.9 1.0
C3C N:HEA603 4.2 33.0 1.0
C3A N:HEA603 4.2 29.6 1.0
C2A N:HEA603 4.2 30.7 1.0
C2D N:HEA603 4.3 29.0 1.0
C3D N:HEA603 4.3 29.1 1.0
C3B N:HEA603 4.3 29.1 1.0
C2B N:HEA603 4.3 27.6 1.0
CU N:CU604 4.9 30.3 1.0

Reference:

N.Yano, K.Muramoto, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara. X-Ray Structure of Cyanide-Bound Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State at 2.0 Angstrom Resolution. Acta Crystallogr F Struct V. 71 726 2015BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 26057802
DOI: 10.1107/S2053230X15007025
Page generated: Sun Dec 13 15:26:42 2020

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