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Zinc 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
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3x2q

Go back to Zinc Binding Sites List in 3x2q
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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
F:Zn101

b:35.2
occ:1.00
 SG F:CYS82 2.3 31.6 1.0
SG F:CYS60 2.3 36.3 1.0
SG F:CYS62 2.3 34.8 1.0
SG F:CYS85 2.4 34.9 1.0
CB F:CYS82 3.2 34.4 1.0
CB F:CYS60 3.2 32.6 1.0
CB F:CYS62 3.4 35.1 1.0
CB F:CYS85 3.4 33.4 1.0
CA F:CYS62 3.6 37.9 1.0
N F:CYS85 3.7 34.2 1.0
CA F:CYS85 4.1 34.8 1.0
N F:CYS62 4.2 37.9 1.0
O F:CYS60 4.4 32.6 1.0
C F:CYS60 4.4 32.8 1.0
CA F:CYS60 4.5 30.9 1.0
CA F:CYS82 4.7 34.4 1.0
C F:SER84 4.7 35.7 1.0
CB F:SER84 4.7 36.8 1.0
OG F:SER84 4.7 38.2 1.0
OG1 F:THR87 4.9 47.4 1.0
C F:CYS85 4.9 35.3 1.0
C F:ILE61 4.9 36.7 1.0
CB F:ILE70 4.9 30.6 1.0
CG2 F:THR87 4.9 40.4 1.0
CG1 F:ILE70 4.9 29.1 1.0
N F:GLY86 5.0 35.6 1.0
C F:CYS62 5.0 39.8 1.0

Zinc binding site 2 out of 2 in 3x2q

Go back to Zinc Binding Sites List in 3x2q
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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
S:Zn101

b:40.0
occ:1.00
 SG S:CYS85 2.3 38.1 1.0
SG S:CYS62 2.3 38.9 1.0
SG S:CYS82 2.3 37.5 1.0
SG S:CYS60 2.4 38.1 1.0
CB S:CYS82 3.1 38.0 1.0
CB S:CYS60 3.2 36.6 1.0
CB S:CYS62 3.3 40.8 1.0
CB S:CYS85 3.4 37.6 1.0
CA S:CYS62 3.7 40.8 1.0
N S:CYS85 3.7 39.4 1.0
N S:CYS62 4.1 39.8 1.0
CA S:CYS85 4.1 39.2 1.0
O S:CYS60 4.4 38.2 1.0
C S:CYS60 4.4 36.7 1.0
CA S:CYS60 4.5 35.9 1.0
OG S:SER84 4.5 40.9 1.0
CA S:CYS82 4.6 39.5 1.0
CB S:SER84 4.6 41.0 1.0
C S:SER84 4.7 41.5 1.0
CG2 S:THR87 4.7 40.6 1.0
C S:ILE61 4.9 39.1 1.0
C S:CYS85 4.9 39.4 1.0
CB S:ILE70 4.9 32.6 1.0
CA S:SER84 4.9 41.2 1.0
OG1 S:THR87 4.9 49.1 1.0
N S:SER84 5.0 42.5 1.0
CG1 S:ILE70 5.0 32.8 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: Wed Dec 16 04:58:28 2020

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