Zinc in PDB 8h8s: Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State, PDB code: 8h8s was solved by K.Muramoto, K.Shinzawa-Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.1, 204.7, 177.9, 90, 90, 90
R / Rfree (%) 12.4 / 15.7

Other elements in 8h8s:

The structure of Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Iron (Fe) 4 atoms
Magnesium (Mg) 2 atoms
Copper (Cu) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State (pdb code 8h8s). 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 Calcium-Bound Fully Reduced State, PDB code: 8h8s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8h8s

Go back to Zinc Binding Sites List in 8h8s
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State


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 Calcium-Bound Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:37.9
occ:1.00
SG F:CYS62 2.3 37.1 1.0
SG F:CYS85 2.3 39.0 1.0
SG F:CYS60 2.3 37.3 1.0
SG F:CYS82 2.3 37.6 1.0
CB F:CYS82 3.2 39.9 1.0
CB F:CYS60 3.3 37.9 1.0
CB F:CYS62 3.3 38.8 1.0
CB F:CYS85 3.4 37.7 1.0
CA F:CYS62 3.6 40.5 1.0
N F:CYS85 3.7 39.5 1.0
CA F:CYS85 4.1 37.3 1.0
N F:CYS62 4.2 36.4 1.0
O F:CYS60 4.4 34.4 1.0
CA F:CYS60 4.4 36.1 1.0
C F:CYS60 4.4 36.1 1.0
OG1 F:THR87 4.5 46.7 0.5
O F:HOH206 4.5 57.5 1.0
CB F:SER84 4.6 38.8 1.0
CA F:CYS82 4.6 35.9 1.0
C F:SER84 4.7 37.1 1.0
CB F:THR87 4.8 38.8 0.5
OG F:SER84 4.8 45.1 1.0
C F:CYS85 4.9 40.3 1.0
C F:ILE61 4.9 37.2 1.0
CG1 F:ILE70 5.0 38.1 1.0
C F:CYS62 5.0 37.8 1.0
N F:GLY86 5.0 39.5 1.0

Zinc binding site 2 out of 2 in 8h8s

Go back to Zinc Binding Sites List in 8h8s
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Calcium-Bound Fully Reduced State


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 Calcium-Bound Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:39.4
occ:1.00
SG S:CYS62 2.3 39.1 1.0
SG S:CYS85 2.3 39.7 1.0
SG S:CYS82 2.4 38.9 1.0
SG S:CYS60 2.4 37.3 1.0
CB S:CYS82 3.1 37.9 1.0
CB S:CYS60 3.2 40.1 1.0
CB S:CYS62 3.4 41.3 1.0
CB S:CYS85 3.4 41.5 1.0
CA S:CYS62 3.7 42.0 1.0
N S:CYS85 3.8 39.0 1.0
CA S:CYS85 4.2 40.6 1.0
N S:CYS62 4.2 38.0 1.0
CG2 S:THR87 4.4 42.9 0.5
CA S:CYS60 4.4 37.4 1.0
C S:CYS60 4.4 34.9 1.0
O S:CYS60 4.5 34.8 1.0
CB S:SER84 4.5 43.2 1.0
O S:HOH211 4.5 60.0 1.0
CA S:CYS82 4.6 39.5 1.0
OG S:SER84 4.7 44.9 1.0
OG1 S:THR87 4.7 39.5 0.5
C S:SER84 4.7 37.4 1.0
CB S:THR87 4.8 38.6 0.5
C S:CYS85 4.9 40.2 1.0
CG1 S:ILE70 4.9 37.2 1.0
C S:ILE61 4.9 36.6 1.0
N S:GLY86 5.0 41.3 1.0
CB S:ILE70 5.0 35.1 1.0
CA S:SER84 5.0 39.0 1.0
N S:SER84 5.0 40.1 1.0
C S:CYS62 5.0 40.0 1.0

Reference:

K.Muramoto, K.Shinzawa-Itoh. Calcium-Bound Structure of Bovine Cytochrome C Oxidase. Biochim Biophys Acta 48956 2023BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 36708913
DOI: 10.1016/J.BBABIO.2023.148956
Page generated: Sat Apr 8 09:17:35 2023

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