Atomistry » Iron » PDB 2xv1-2yde » 2y69
Atomistry »
  Iron »
    PDB 2xv1-2yde »
      2y69 »

Iron in PDB 2y69: Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen

Enzymatic activity of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen, PDB code: 2y69 was solved by V.R.I.Kaila, E.Oksanen, A.Goldman, M.I.Verkhovsky, D.Sundholm, M.Wikstrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.15 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.697, 206.991, 178.251, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.5

Other elements in 2y69:

The structure of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen (pdb code 2y69). 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 Re-Refined with Molecular Oxygen, PDB code: 2y69:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2y69

Go back to Iron Binding Sites List in 2y69
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:26.2
occ:1.00
 FE A:HEA515 0.0 26.2 1.0
NE2 A:HIS378 1.9 24.5 1.0
NE2 A:HIS61 1.9 22.7 1.0
ND A:HEA515 2.0 25.4 1.0
NB A:HEA515 2.0 26.3 1.0
NA A:HEA515 2.0 28.7 1.0
NC A:HEA515 2.0 24.8 1.0
CE1 A:HIS61 2.9 26.0 1.0
CE1 A:HIS378 2.9 28.1 1.0
CD2 A:HIS378 3.0 26.9 1.0
C4A A:HEA515 3.0 30.2 1.0
C4C A:HEA515 3.0 25.1 1.0
C1D A:HEA515 3.0 25.1 1.0
C4D A:HEA515 3.0 23.6 1.0
C1B A:HEA515 3.0 29.3 1.0
CD2 A:HIS61 3.0 27.6 1.0
C1C A:HEA515 3.0 25.5 1.0
C4B A:HEA515 3.1 26.9 1.0
C1A A:HEA515 3.1 27.7 1.0
CHB A:HEA515 3.4 28.8 1.0
CHD A:HEA515 3.4 24.0 1.0
CHC A:HEA515 3.4 22.0 1.0
CHA A:HEA515 3.5 24.4 1.0
ND1 A:HIS378 4.0 24.2 1.0
ND1 A:HIS61 4.0 24.9 1.0
CG A:HIS378 4.1 25.2 1.0
CG A:HIS61 4.1 25.7 1.0
C3A A:HEA515 4.3 29.4 1.0
C2D A:HEA515 4.3 24.3 1.0
C3C A:HEA515 4.3 24.9 1.0
C3D A:HEA515 4.3 26.2 1.0
C2B A:HEA515 4.3 26.0 1.0
C2C A:HEA515 4.3 26.0 1.0
C3B A:HEA515 4.4 25.7 1.0
C2A A:HEA515 4.4 30.3 1.0
CE1 A:PHE377 5.0 29.2 1.0

Iron binding site 2 out of 4 in 2y69

Go back to Iron Binding Sites List in 2y69
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:26.4
occ:1.00
 FE A:HEA516 0.0 26.4 1.0
ND A:HEA516 2.0 24.0 1.0
NA A:HEA516 2.0 24.9 1.0
NB A:HEA516 2.0 26.0 1.0
NE2 A:HIS376 2.0 25.8 1.0
NC A:HEA516 2.0 27.4 1.0
O2 A:OXY1515 2.2 32.3 1.0
CE1 A:HIS376 2.9 31.2 1.0
C4D A:HEA516 3.0 26.4 1.0
C1A A:HEA516 3.0 24.1 1.0
C4A A:HEA516 3.0 22.2 1.0
C4B A:HEA516 3.0 26.3 1.0
C1C A:HEA516 3.0 25.1 1.0
C1D A:HEA516 3.0 26.8 1.0
C4C A:HEA516 3.0 22.7 1.0
CD2 A:HIS376 3.0 29.2 1.0
C1B A:HEA516 3.1 26.1 1.0
O1 A:OXY1515 3.1 41.0 1.0
CHA A:HEA516 3.4 23.9 1.0
CHC A:HEA516 3.4 25.2 1.0
CHB A:HEA516 3.4 23.2 1.0
CHD A:HEA516 3.5 21.1 1.0
ND1 A:HIS376 4.1 29.8 1.0
CG A:HIS376 4.2 28.1 1.0
C3A A:HEA516 4.2 23.4 1.0
C2D A:HEA516 4.3 23.6 1.0
C2A A:HEA516 4.3 26.3 1.0
C3D A:HEA516 4.3 24.6 1.0
C3B A:HEA516 4.3 27.0 1.0
C2B A:HEA516 4.3 25.6 1.0
C2C A:HEA516 4.3 29.0 1.0
C3C A:HEA516 4.3 25.5 1.0
CU A:CU517 4.9 28.5 1.0

Iron binding site 3 out of 4 in 2y69

Go back to Iron Binding Sites List in 2y69
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:31.4
occ:1.00
 FE N:HEA515 0.0 31.4 1.0
NE2 N:HIS378 1.9 22.4 1.0
NE2 N:HIS61 2.0 23.8 1.0
NC N:HEA515 2.0 30.6 1.0
NA N:HEA515 2.0 34.4 1.0
NB N:HEA515 2.0 35.6 1.0
ND N:HEA515 2.0 32.2 1.0
CD2 N:HIS378 2.9 31.2 1.0
CD2 N:HIS61 2.9 33.3 1.0
CE1 N:HIS378 2.9 29.2 1.0
C4C N:HEA515 3.0 45.9 1.0
C4A N:HEA515 3.0 36.2 1.0
CE1 N:HIS61 3.0 38.4 1.0
C1B N:HEA515 3.0 32.6 1.0
C1A N:HEA515 3.0 39.8 1.0
C1C N:HEA515 3.0 40.5 1.0
C1D N:HEA515 3.0 54.2 1.0
C4B N:HEA515 3.1 35.9 1.0
C4D N:HEA515 3.1 29.3 1.0
CHB N:HEA515 3.4 40.0 1.0
CHD N:HEA515 3.4 36.0 1.0
CHC N:HEA515 3.5 32.0 1.0
CHA N:HEA515 3.5 34.7 1.0
ND1 N:HIS378 4.0 27.0 1.0
CG N:HIS378 4.0 22.1 1.0
ND1 N:HIS61 4.1 28.3 1.0
CG N:HIS61 4.1 29.0 1.0
C3A N:HEA515 4.2 44.0 1.0
C3C N:HEA515 4.2 35.7 1.0
C2B N:HEA515 4.3 53.7 1.0
C2C N:HEA515 4.3 38.6 1.0
C2A N:HEA515 4.3 45.6 1.0
C3B N:HEA515 4.4 34.4 1.0
C2D N:HEA515 4.4 26.6 1.0
C3D N:HEA515 4.4 25.6 1.0
CE1 N:PHE377 5.0 33.8 1.0

Iron binding site 4 out of 4 in 2y69

Go back to Iron Binding Sites List in 2y69
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:34.7
occ:1.00
 FE N:HEA516 0.0 34.7 1.0
NC N:HEA516 2.0 37.5 1.0
ND N:HEA516 2.0 33.3 1.0
NB N:HEA516 2.0 35.8 1.0
NA N:HEA516 2.0 39.4 1.0
NE2 N:HIS376 2.0 44.4 1.0
O1 N:OXY1515 2.4 31.2 1.0
CE1 N:HIS376 2.9 44.7 1.0
C4D N:HEA516 3.0 32.2 1.0
C1C N:HEA516 3.0 27.9 1.0
C1A N:HEA516 3.0 29.0 1.0
C4A N:HEA516 3.0 26.3 1.0
O2 N:OXY1515 3.0 33.9 1.0
C1B N:HEA516 3.0 29.6 1.0
C4C N:HEA516 3.0 30.8 1.0
C4B N:HEA516 3.0 32.8 1.0
C1D N:HEA516 3.0 36.3 1.0
CD2 N:HIS376 3.1 34.6 1.0
CHA N:HEA516 3.4 26.9 1.0
CHC N:HEA516 3.4 31.1 1.0
CHB N:HEA516 3.4 21.4 1.0
CHD N:HEA516 3.5 30.0 1.0
ND1 N:HIS376 4.1 34.6 1.0
CG N:HIS376 4.2 35.8 1.0
C3A N:HEA516 4.3 27.1 1.0
C3C N:HEA516 4.3 34.5 1.0
C2C N:HEA516 4.3 40.6 1.0
C2D N:HEA516 4.3 26.5 1.0
C2B N:HEA516 4.3 31.7 1.0
C3D N:HEA516 4.3 29.2 1.0
C3B N:HEA516 4.3 29.2 1.0
C2A N:HEA516 4.3 31.1 1.0
CU N:CU517 4.9 32.4 1.0
CG2 N:VAL243 4.9 34.6 1.0

Reference:

V.R.I.Kaila, E.Oksanen, A.Goldman, D.A.Bloch, M.I.Verkhovsky, D.Sundholm, M.Wikstrom. A Combined Quantum Chemical and Crystallographic Study on the Oxidized Binuclear Center of Cytochrome C Oxidase. Biochim.Biophys.Acta V.1807 769 2011.
ISSN: ISSN 0006-3002
PubMed: 21211513
DOI: 10.1016/J.BBABIO.2010.12.016
Page generated: Sun Aug 4 05:07:51 2024

Last articles

As in 2GWS
As in 2H5K
As in 2GBM
As in 2GWN
As in 2G6O
As in 2C7V
As in 2CJW
As in 2E11
As in 2FAU
As in 2DYB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy