Zinc in PDB 7d5w: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution, PDB code: 7d5w 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) 39.92 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.435, 203.092, 177.794, 90, 90, 90
R / Rfree (%) 15.4 / 18.4

Other elements in 7d5w:

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 O at 1.84 Angstrom Resolution (pdb code 7d5w). 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 O at 1.84 Angstrom Resolution, PDB code: 7d5w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7d5w

Go back to Zinc Binding Sites List in 7d5w
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:26.2
occ:1.00
SG F:CYS60 2.3 28.1 1.0
SG F:CYS62 2.3 28.4 1.0
SG F:CYS85 2.3 30.5 1.0
SG F:CYS82 2.4 26.5 1.0
CB F:CYS82 3.2 24.0 1.0
CB F:CYS60 3.2 31.4 1.0
CB F:CYS62 3.3 27.1 1.0
CB F:CYS85 3.4 29.9 1.0
CA F:CYS62 3.6 30.0 1.0
N F:CYS85 3.7 26.8 1.0
CA F:CYS85 4.1 30.4 1.0
N F:CYS62 4.2 28.1 1.0
O F:CYS60 4.4 25.2 1.0
C F:CYS60 4.4 28.8 1.0
CA F:CYS60 4.4 25.6 1.0
CB F:SER84 4.5 32.1 1.0
CG2 F:THR87 4.6 46.6 0.5
OG1 F:THR87 4.6 49.4 0.5
O F:HOH226 4.6 48.7 1.0
CA F:CYS82 4.6 27.6 1.0
C F:SER84 4.8 32.9 1.0
OG F:SER84 4.8 37.4 1.0
C F:CYS85 4.8 34.0 1.0
C F:ILE61 4.9 32.4 1.0
C F:CYS62 4.9 35.4 1.0
CB F:ILE70 4.9 23.5 1.0
CG1 F:ILE70 4.9 23.4 1.0
N F:GLY86 5.0 27.8 1.0
CG2 F:THR87 5.0 26.2 0.5

Zinc binding site 2 out of 2 in 7d5w

Go back to Zinc Binding Sites List in 7d5w
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:25.8
occ:1.00
SG S:CYS60 2.3 27.2 1.0
SG S:CYS62 2.3 27.9 1.0
SG S:CYS82 2.3 29.2 1.0
SG S:CYS85 2.3 28.7 1.0
CB S:CYS82 3.1 27.0 1.0
CB S:CYS60 3.2 28.2 1.0
CB S:CYS62 3.3 28.1 1.0
CB S:CYS85 3.4 28.5 1.0
CA S:CYS62 3.6 27.6 1.0
N S:CYS85 3.7 31.0 1.0
CA S:CYS85 4.1 28.3 1.0
N S:CYS62 4.1 32.5 1.0
CA S:CYS60 4.4 24.4 1.0
O S:CYS60 4.4 24.5 1.0
C S:CYS60 4.4 30.2 1.0
CB S:SER84 4.5 28.1 1.0
CA S:CYS82 4.6 26.2 1.0
O S:HOH219 4.6 38.6 1.0
C S:SER84 4.7 32.9 1.0
OG1 S:THR87 4.7 63.6 1.0
OG S:SER84 4.8 39.7 1.0
C S:CYS85 4.9 32.9 1.0
C S:ILE61 4.9 29.8 1.0
C S:CYS62 4.9 36.6 1.0
N S:SER84 5.0 31.4 1.0
N S:GLY86 5.0 27.3 1.0
CA S:SER84 5.0 27.9 1.0
CB S:THR87 5.0 33.1 1.0
CB S:ILE70 5.0 26.2 1.0
CG1 S:ILE70 5.0 23.3 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 18:01:00 2021

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