Zinc in PDB 7cp5: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution, PDB code: 7cp5 was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.91 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.589, 203.218, 177.702, 90, 90, 90
R / Rfree (%) 16 / 18.9

Other elements in 7cp5:

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 Angstrom Resolution (pdb code 7cp5). 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution, PDB code: 7cp5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7cp5

Go back to Zinc Binding Sites List in 7cp5
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:26.0
occ:1.00
SG F:CYS60 2.3 28.3 1.0
SG F:CYS62 2.3 27.8 1.0
SG F:CYS82 2.3 26.6 1.0
SG F:CYS85 2.3 29.6 1.0
CB F:CYS82 3.2 23.4 1.0
CB F:CYS60 3.2 31.8 1.0
CB F:CYS62 3.3 25.1 1.0
CB F:CYS85 3.4 27.2 1.0
CA F:CYS62 3.6 27.8 1.0
N F:CYS85 3.7 27.0 1.0
OG1 F:THR87 4.0 75.5 0.5
CA F:CYS85 4.1 30.0 1.0
N F:CYS62 4.2 29.2 1.0
O F:CYS60 4.3 26.0 1.0
CA F:CYS60 4.4 27.5 1.0
C F:CYS60 4.4 31.3 1.0
CB F:SER84 4.5 27.2 1.0
O F:HOH219 4.6 42.5 1.0
CA F:CYS82 4.6 25.2 1.0
C F:SER84 4.7 32.2 1.0
OG F:SER84 4.7 34.8 1.0
C F:CYS85 4.8 28.9 1.0
C F:ILE61 4.9 32.3 1.0
CG2 F:THR87 4.9 38.0 0.5
C F:CYS62 4.9 36.1 1.0
CG1 F:ILE70 4.9 23.6 1.0
CG2 F:THR87 4.9 20.8 0.5
N F:SER84 4.9 28.9 1.0
N F:GLY86 4.9 27.6 1.0
CA F:SER84 5.0 27.4 1.0
CB F:ILE70 5.0 24.2 1.0

Zinc binding site 2 out of 2 in 7cp5

Go back to Zinc Binding Sites List in 7cp5
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of E at 1.76 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 A Catalytic Intermediate of E at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:26.6
occ:1.00
SG S:CYS60 2.3 27.7 1.0
SG S:CYS82 2.3 29.2 1.0
SG S:CYS62 2.3 28.4 1.0
SG S:CYS85 2.3 29.8 1.0
CB S:CYS82 3.2 23.6 1.0
CB S:CYS60 3.3 28.8 1.0
CB S:CYS62 3.3 27.5 1.0
CB S:CYS85 3.4 28.8 1.0
CA S:CYS62 3.6 29.3 1.0
N S:CYS85 3.7 29.6 1.0
CA S:CYS85 4.1 26.5 1.0
N S:CYS62 4.2 33.3 1.0
O S:CYS60 4.4 24.9 1.0
CB S:SER84 4.4 30.6 1.0
C S:CYS60 4.4 30.3 1.0
CA S:CYS60 4.4 28.4 1.0
OG1 S:THR87 4.6 48.8 1.0
CA S:CYS82 4.6 25.6 1.0
O S:HOH223 4.7 37.3 1.0
C S:SER84 4.7 29.6 1.0
OG S:SER84 4.7 36.1 1.0
C S:CYS85 4.9 30.3 1.0
C S:ILE61 4.9 28.1 1.0
CA S:SER84 4.9 28.1 1.0
N S:SER84 4.9 32.6 1.0
CG1 S:ILE70 5.0 27.1 1.0
N S:GLY86 5.0 26.7 1.0
C S:CYS62 5.0 33.2 1.0
CB S:ILE70 5.0 27.1 1.0

Reference:

A.Shimada, F.Hara, K.Shinzawa-Itoh, N.Kanehisa, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. Critical Roles of the Cub Site in Efficient Proton Pumping As Revealed By Crystal Structures of Mammalian Cytochrome C Oxidase Catalytic Intermediates J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Sat Aug 21 18:00:39 2021

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