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Zinc in PDB 5xdq: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution, PDB code: 5xdq was solved by F.J.Luo, A.Shimada, N.Hagimoto, S.Shimada, 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) 134.45 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.307, 205.904, 177.526, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19

Other elements in 5xdq:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution (pdb code 5xdq). 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 in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution, PDB code: 5xdq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5xdq

Go back to Zinc Binding Sites List in 5xdq
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


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 in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:35.9
occ:1.00
SG F:CYS85 2.4 35.2 1.0
SG F:CYS82 2.4 34.5 1.0
SG F:CYS60 2.4 34.5 1.0
SG F:CYS62 2.4 35.8 1.0
CB F:CYS82 3.2 35.1 1.0
CB F:CYS60 3.3 34.9 1.0
CB F:CYS85 3.4 34.5 1.0
CB F:CYS62 3.4 35.5 1.0
CA F:CYS62 3.6 34.8 1.0
N F:CYS85 3.8 34.4 1.0
N F:CYS62 4.1 34.5 1.0
CA F:CYS85 4.1 34.8 1.0
O F:CYS60 4.4 32.2 1.0
C F:CYS60 4.4 31.2 1.0
CA F:CYS60 4.5 32.4 1.0
CB F:SER84 4.5 38.1 1.0
OG1 F:THR87 4.6 60.5 1.0
O F:HOH210 4.6 62.8 1.0
CA F:CYS82 4.6 35.2 1.0
OG F:SER84 4.7 42.2 1.0
C F:SER84 4.8 35.7 1.0
C F:CYS85 4.9 35.1 1.0
C F:ILE61 4.9 32.9 1.0
CB F:ILE70 4.9 28.6 1.0
CG1 F:ILE70 4.9 29.0 1.0
N F:GLY86 5.0 32.0 1.0
CA F:SER84 5.0 37.6 1.0
C F:CYS62 5.0 37.9 1.0
CG2 F:THR87 5.0 41.1 1.0
N F:SER84 5.0 36.8 1.0

Zinc binding site 2 out of 2 in 5xdq

Go back to Zinc Binding Sites List in 5xdq
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


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 in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:37.4
occ:1.00
SG S:CYS85 2.4 36.9 1.0
SG S:CYS82 2.4 35.1 1.0
SG S:CYS62 2.4 36.1 1.0
SG S:CYS60 2.4 35.3 1.0
CB S:CYS82 3.1 35.4 1.0
CB S:CYS60 3.3 36.5 1.0
CB S:CYS62 3.4 36.1 1.0
CB S:CYS85 3.4 37.9 1.0
CA S:CYS62 3.6 36.2 1.0
N S:CYS85 3.7 36.3 1.0
N S:CYS62 4.1 37.3 1.0
CA S:CYS85 4.1 35.7 1.0
OG1 S:THR87 4.2 59.5 1.0
O S:CYS60 4.4 34.8 1.0
C S:CYS60 4.5 31.8 1.0
CB S:SER84 4.5 36.7 1.0
CA S:CYS60 4.5 34.1 1.0
CA S:CYS82 4.6 36.1 1.0
O S:HOH210 4.7 58.3 1.0
C S:SER84 4.7 36.1 1.0
OG S:SER84 4.8 42.4 1.0
C S:CYS85 4.8 34.9 1.0
C S:ILE61 4.9 36.8 1.0
CG1 S:ILE70 4.9 34.0 1.0
CA S:SER84 4.9 36.0 1.0
N S:GLY86 4.9 35.8 1.0
N S:SER84 4.9 38.4 1.0
CB S:ILE70 4.9 29.7 1.0
C S:CYS62 5.0 37.7 1.0

Reference:

F.Luo, K.Shinzawa-Itoh, K.Hagimoto, A.Shimada, S.Shimada, E.Yamashita, S.Yoshikawa, T.Tsukihara. Structure of Bovine Cytochrome C Oxidase Crystallized at A Neutral pH Using A Fluorinated Detergent. Acta Crystallogr F Struct V. 73 416 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28695851
DOI: 10.1107/S2053230X17008834
Page generated: Wed Dec 16 11:20:02 2020

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