Atomistry » Iron » PDB 3x20-3zjo » 3x2q
Atomistry »
  Iron »
    PDB 3x20-3zjo »
      3x2q »

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 Aug 4 22:58:38 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy