Zinc in PDB 7ypy: Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 7ypy was solved by A.Shimada, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.96 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.938, 204.4, 177.896, 90, 90, 90
R / Rfree (%) 15.9 / 17.7

Other elements in 7ypy:

The structure of Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 Angstrom Resolution (pdb code 7ypy). 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 Fully Oxidized State at 1.5 Angstrom Resolution, PDB code: 7ypy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7ypy

Go back to Zinc Binding Sites List in 7ypy
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:25.1
occ:1.00
SG F:CYS62 2.3 25.6 1.0
SG F:CYS85 2.3 26.2 1.0
SG F:CYS82 2.3 24.9 1.0
SG F:CYS60 2.4 25.5 1.0
CB F:CYS82 3.1 24.9 1.0
CB F:CYS62 3.3 25.7 1.0
CB F:CYS60 3.3 26.6 1.0
CB F:CYS85 3.3 26.3 1.0
CA F:CYS62 3.6 28.0 1.0
N F:CYS85 3.7 26.8 1.0
CA F:CYS85 4.1 27.2 1.0
N F:CYS62 4.2 25.6 1.0
O F:CYS60 4.4 24.2 1.0
CB F:SER84 4.4 25.9 1.0
CG2 F:THR87 4.4 26.8 0.5
CA F:CYS60 4.5 25.2 1.0
C F:CYS60 4.5 23.3 1.0
CA F:CYS82 4.6 25.8 1.0
O F:HOH216 4.6 36.8 1.0
OG1 F:THR87 4.6 29.7 0.5
C F:SER84 4.7 29.4 1.0
OG F:SER84 4.8 33.8 1.0
C F:CYS85 4.8 25.9 1.0
N F:GLY86 4.9 25.8 1.0
C F:CYS62 4.9 25.3 1.0
C F:ILE61 4.9 27.5 1.0
CA F:SER84 5.0 25.1 1.0
CB F:ILE70 5.0 22.8 1.0
CG1 F:ILE70 5.0 23.1 1.0
N F:SER84 5.0 27.0 1.0

Zinc binding site 2 out of 2 in 7ypy

Go back to Zinc Binding Sites List in 7ypy
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in Fully Oxidized State at 1.5 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 Fully Oxidized State at 1.5 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:25.6
occ:1.00
SG S:CYS62 2.3 26.7 1.0
SG S:CYS82 2.3 26.5 1.0
SG S:CYS85 2.3 27.4 1.0
SG S:CYS60 2.3 26.5 1.0
CB S:CYS82 3.1 26.0 1.0
CB S:CYS60 3.3 25.7 1.0
CB S:CYS62 3.3 25.9 1.0
CB S:CYS85 3.3 27.3 1.0
CA S:CYS62 3.7 25.5 1.0
N S:CYS85 3.7 27.6 1.0
CA S:CYS85 4.1 30.2 1.0
N S:CYS62 4.3 25.0 1.0
OG1 S:THR87 4.3 39.1 0.5
CB S:SER84 4.4 28.5 1.0
O S:CYS60 4.4 24.3 1.0
CA S:CYS60 4.5 23.3 1.0
C S:CYS60 4.5 25.2 1.0
CA S:CYS82 4.6 25.9 1.0
O S:HOH221 4.7 39.4 1.0
CG2 S:THR87 4.7 35.7 0.5
C S:SER84 4.7 30.4 1.0
OG S:SER84 4.8 36.0 1.0
C S:CYS85 4.9 30.1 1.0
CG1 S:ILE70 4.9 24.9 1.0
N S:GLY86 4.9 27.9 1.0
CB S:ILE70 5.0 22.3 1.0
CA S:SER84 5.0 27.7 1.0
C S:ILE61 5.0 28.3 1.0
C S:CYS62 5.0 29.9 1.0
N S:SER84 5.0 27.6 1.0

Reference:

N.Yano, K.Muramoto, A.Shimada, K.Shinzawa-Itoh, T.Tsukihara, S.Yoshikawa. The MG2+-Containing Water Cluster of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J. Biol. Chem. V. 291 23882 2016.
ISSN: ESSN 1083-351X
PubMed: 27605664
DOI: 10.1074/JBC.M115.711770
Page generated: Sat Apr 8 06:22:15 2023

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