Zinc in PDB 7d5x: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution, PDB code: 7d5x 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) 39.70 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.767, 203.304, 177.566, 90, 90, 90
R / Rfree (%) 15.6 / 18.4

Other elements in 7d5x:

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution (pdb code 7d5x). 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, IO10, at 1.74 Angstrom Resolution, PDB code: 7d5x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7d5x

Go back to Zinc Binding Sites List in 7d5x
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:26.5
occ:1.00
SG F:CYS60 2.3 27.7 1.0
SG F:CYS62 2.3 29.1 1.0
SG F:CYS82 2.3 27.1 1.0
SG F:CYS85 2.3 29.5 1.0
CB F:CYS82 3.2 27.9 1.0
CB F:CYS60 3.2 29.8 1.0
CB F:CYS62 3.3 26.3 1.0
CB F:CYS85 3.4 28.8 1.0
CA F:CYS62 3.6 29.6 1.0
N F:CYS85 3.6 28.1 1.0
CA F:CYS85 4.1 27.4 1.0
N F:CYS62 4.1 27.0 1.0
O F:CYS60 4.4 25.9 1.0
CA F:CYS60 4.4 29.3 1.0
C F:CYS60 4.4 30.5 1.0
O F:HOH242 4.5 44.5 1.0
CB F:SER84 4.5 30.4 1.0
CA F:CYS82 4.6 25.3 1.0
C F:SER84 4.7 34.8 1.0
OG F:SER84 4.8 35.6 1.0
OG1 F:THR87 4.8 48.1 1.0
C F:CYS85 4.8 31.6 1.0
C F:ILE61 4.9 27.6 1.0
C F:CYS62 4.9 33.8 1.0
N F:GLY86 4.9 29.3 1.0
N F:SER84 4.9 26.9 1.0
CG1 F:ILE70 4.9 26.1 1.0
CA F:SER84 4.9 28.4 1.0
CB F:ILE70 4.9 26.2 1.0

Zinc binding site 2 out of 2 in 7d5x

Go back to Zinc Binding Sites List in 7d5x
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:27.1
occ:1.00
SG S:CYS85 2.3 29.6 1.0
SG S:CYS60 2.3 26.8 1.0
SG S:CYS82 2.3 28.9 1.0
SG S:CYS62 2.4 28.8 1.0
CB S:CYS82 3.2 29.3 1.0
CB S:CYS60 3.2 29.1 1.0
CB S:CYS62 3.3 29.1 1.0
CB S:CYS85 3.4 29.7 1.0
N S:CYS85 3.6 29.5 1.0
CA S:CYS62 3.7 26.8 1.0
CA S:CYS85 4.1 28.9 1.0
N S:CYS62 4.2 29.6 1.0
CB S:SER84 4.3 30.8 1.0
O S:CYS60 4.4 23.6 1.0
C S:CYS60 4.4 27.3 1.0
CA S:CYS60 4.5 27.3 1.0
OG1 S:THR87 4.6 50.7 1.0
O S:HOH218 4.6 38.2 1.0
CA S:CYS82 4.6 27.4 1.0
C S:SER84 4.7 33.0 1.0
OG S:SER84 4.8 34.5 1.0
C S:CYS85 4.8 31.8 1.0
CA S:SER84 4.9 31.1 1.0
N S:GLY86 4.9 28.9 1.0
C S:ILE61 4.9 27.2 1.0
N S:SER84 4.9 28.8 1.0
CB S:ILE70 5.0 25.8 1.0
C S:CYS62 5.0 33.6 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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