Zinc in PDB 7coh: Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

Enzymatic activity of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

All present enzymatic activity of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State:
7.1.1.9;

Protein crystallography data

The structure of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 7coh was solved by K.Shinzawa-Itoh, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.998, 204.193, 177.759, 90, 90, 90
R / Rfree (%) 14.9 / 17

Other elements in 7coh:

The structure of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 7coh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 7coh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7coh

Go back to Zinc Binding Sites List in 7coh
Zinc binding site 1 out of 2 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn99

b:24.4
occ:1.00
SG F:CYS62 2.3 24.6 1.0
SG F:CYS82 2.3 23.8 1.0
SG F:CYS85 2.3 25.4 1.0
SG F:CYS60 2.4 24.0 1.0
CB F:CYS82 3.1 24.8 1.0
CB F:CYS60 3.2 24.7 1.0
CB F:CYS62 3.3 24.8 1.0
CB F:CYS85 3.4 25.4 1.0
CA F:CYS62 3.6 25.4 1.0
N F:CYS85 3.7 25.5 1.0
CA F:CYS85 4.1 24.9 1.0
N F:CYS62 4.2 24.3 1.0
OG1 F:THR87 4.3 40.8 0.5
CA F:CYS60 4.4 22.3 1.0
O F:CYS60 4.4 22.3 1.0
CB F:SER84 4.4 24.9 1.0
C F:CYS60 4.4 22.2 1.0
CA F:CYS82 4.6 25.9 1.0
O F:HOH1269 4.6 39.7 1.0
OG F:SER84 4.7 32.3 1.0
CB F:THR87 4.8 27.1 0.5
C F:SER84 4.8 23.9 1.0
C F:CYS85 4.9 25.2 1.0
N F:GLY86 4.9 25.4 1.0
C F:ILE61 5.0 25.1 1.0
CB F:ILE70 5.0 20.1 1.0
C F:CYS62 5.0 26.6 1.0
CA F:SER84 5.0 27.2 1.0
N F:SER84 5.0 24.8 1.0
OG1 F:THR87 5.0 31.5 0.5

Zinc binding site 2 out of 2 in 7coh

Go back to Zinc Binding Sites List in 7coh
Zinc binding site 2 out of 2 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn99

b:25.3
occ:1.00
SG S:CYS62 2.3 25.2 1.0
SG S:CYS82 2.3 24.9 1.0
SG S:CYS85 2.4 26.4 1.0
SG S:CYS60 2.4 24.4 1.0
CB S:CYS82 3.2 26.0 1.0
CB S:CYS60 3.2 24.3 1.0
CB S:CYS62 3.3 27.3 1.0
CB S:CYS85 3.3 27.8 1.0
CA S:CYS62 3.6 26.3 1.0
N S:CYS85 3.7 26.4 1.0
CA S:CYS85 4.1 27.2 1.0
N S:CYS62 4.2 25.0 1.0
O S:CYS60 4.4 21.9 1.0
CA S:CYS60 4.4 22.2 1.0
CB S:SER84 4.4 26.8 1.0
C S:CYS60 4.5 25.0 1.0
CG2 S:THR87 4.5 24.4 0.5
O S:HOH2269 4.6 40.3 1.0
CA S:CYS82 4.6 25.5 1.0
OG S:SER84 4.7 32.8 1.0
CB S:THR87 4.7 29.9 0.5
C S:SER84 4.7 26.5 1.0
OG1 S:THR87 4.8 35.2 0.5
C S:CYS85 4.9 27.9 1.0
C S:ILE61 5.0 24.3 1.0
N S:GLY86 5.0 27.0 1.0
CA S:SER84 5.0 28.3 1.0
CB S:ILE70 5.0 20.8 1.0
N S:SER84 5.0 26.7 1.0
C S:CYS62 5.0 29.7 1.0

Reference:

K.Shinzawa-Itoh, M.Hatanaka, K.Fujita, N.Yano, Y.Ogasawara, J.Iwata, E.Yamashita, T.Tsukihara, S.Yoshikawa, K.Muramoto. The 1.3-A Resolution Structure of Bovine Cytochrome C Oxidase Suggests A Dimerization Mechanism Biochim.Biophys.Acta 2021.
ISSN: ISSN 0006-3002
DOI: 10.1016/J.BBADVA.2021.100009
Page generated: Sat Apr 17 17:47:30 2021

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