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Zinc 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
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen, PDB code: 2y69:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2y69

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
F:Zn1097

b:35.5
occ:1.00
SG F:CYS82 2.3 32.3 1.0
SG F:CYS60 2.3 37.3 1.0
SG F:CYS62 2.3 33.5 1.0
SG F:CYS85 2.4 35.6 1.0
CB F:CYS82 3.2 37.6 1.0
CB F:CYS60 3.4 33.9 1.0
CB F:CYS62 3.4 26.9 1.0
CB F:CYS85 3.4 30.1 1.0
CA F:CYS62 3.6 40.8 1.0
N F:CYS85 3.7 31.6 1.0
N F:CYS62 4.0 37.6 1.0
CA F:CYS85 4.1 28.1 1.0
O F:CYS60 4.3 40.6 1.0
C F:CYS60 4.5 30.9 1.0
CA F:CYS60 4.5 25.6 1.0
OG F:SER84 4.6 39.1 1.0
CB F:SER84 4.6 40.2 1.0
CA F:CYS82 4.7 38.9 1.0
C F:SER84 4.7 33.7 1.0
C F:CYS85 4.8 45.1 1.0
CB F:ILE70 4.8 29.4 1.0
CG1 F:ILE70 4.9 29.6 1.0
C F:ILE61 4.9 39.7 1.0
OG1 F:THR87 4.9 49.8 1.0
C F:CYS62 5.0 64.8 1.0
N F:GLY86 5.0 42.0 1.0

Zinc binding site 2 out of 2 in 2y69

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
S:Zn1097

b:39.4
occ:1.00
SG S:CYS82 2.3 35.7 1.0
SG S:CYS85 2.3 39.5 1.0
SG S:CYS60 2.4 38.0 1.0
SG S:CYS62 2.4 39.2 1.0
CB S:CYS82 3.1 32.9 1.0
CB S:CYS60 3.3 40.6 1.0
CB S:CYS62 3.4 29.9 1.0
CB S:CYS85 3.4 31.4 1.0
N S:CYS85 3.6 38.9 1.0
CA S:CYS62 3.6 39.2 1.0
N S:CYS62 4.1 42.7 1.0
CA S:CYS85 4.1 31.1 1.0
O S:CYS60 4.4 34.1 1.0
C S:CYS60 4.4 43.9 1.0
CA S:CYS60 4.5 36.9 1.0
CB S:SER84 4.5 37.6 1.0
CA S:CYS82 4.6 39.3 1.0
OG1 S:THR87 4.6 70.7 1.0
C S:SER84 4.7 44.4 1.0
OG S:SER84 4.7 42.9 1.0
CG2 S:THR87 4.7 41.3 1.0
C S:CYS85 4.8 31.4 1.0
N S:GLY86 4.8 45.0 1.0
C S:ILE61 4.9 54.5 1.0
CA S:SER84 4.9 40.5 1.0
CG1 S:ILE70 4.9 37.3 1.0
CB S:ILE70 4.9 35.7 1.0
N S:SER84 4.9 47.5 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: Wed Dec 16 04:01:36 2020

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