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Zinc in PDB 2dyr: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 2dyr was solved by K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, T.Kurauchi, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.590, 205.140, 178.250, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.7

Other elements in 2dyr:

The structure of Bovine Heart Cytochrome C Oxidase at 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (pdb code 2dyr). 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 at the Fully Oxidized State, PDB code: 2dyr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2dyr

Go back to Zinc Binding Sites List in 2dyr
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn99

b:25.6
occ:1.00
SG F:CYS82 2.2 26.5 1.0
SG F:CYS60 2.2 26.3 1.0
SG F:CYS62 2.2 25.6 1.0
SG F:CYS85 2.3 25.6 1.0
CB F:CYS82 3.2 28.2 1.0
CB F:CYS60 3.3 22.7 1.0
CB F:CYS62 3.4 24.8 1.0
CB F:CYS85 3.4 25.9 1.0
CA F:CYS62 3.6 27.7 1.0
N F:CYS85 3.7 27.8 1.0
N F:CYS62 3.9 27.7 1.0
CA F:CYS85 4.1 28.4 1.0
O F:CYS60 4.3 24.0 1.0
C F:CYS60 4.4 24.0 1.0
CB F:SER84 4.5 27.3 1.0
CA F:CYS60 4.5 21.4 1.0
O F:HOH2337 4.5 47.4 1.0
OG F:SER84 4.6 30.4 1.0
CA F:CYS82 4.7 26.5 1.0
C F:SER84 4.7 26.3 1.0
C F:CYS85 4.8 30.1 1.0
CG2 F:THR87 4.8 32.6 1.0
C F:ILE61 4.8 27.3 1.0
C F:CYS62 4.9 31.0 1.0
N F:GLY86 4.9 31.2 1.0
CA F:SER84 5.0 26.8 1.0
CB F:ILE70 5.0 22.6 1.0
CG1 F:ILE70 5.0 21.5 1.0

Zinc binding site 2 out of 2 in 2dyr

Go back to Zinc Binding Sites List in 2dyr
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn99

b:27.1
occ:1.00
SG S:CYS82 2.2 24.7 1.0
SG S:CYS60 2.3 22.1 1.0
SG S:CYS62 2.3 29.2 1.0
SG S:CYS85 2.3 27.3 1.0
CB S:CYS82 3.1 26.4 1.0
CB S:CYS60 3.3 23.3 1.0
CB S:CYS62 3.4 27.7 1.0
CB S:CYS85 3.4 25.7 1.0
CA S:CYS62 3.7 27.0 1.0
N S:CYS85 3.7 27.3 1.0
N S:CYS62 4.0 28.5 1.0
CA S:CYS85 4.1 27.8 1.0
O S:CYS60 4.3 25.0 1.0
OG1 S:THR87 4.4 37.0 1.0
C S:CYS60 4.4 25.1 1.0
CA S:CYS60 4.5 23.9 1.0
CB S:SER84 4.5 28.6 1.0
CA S:CYS82 4.6 26.2 1.0
O S:HOH3337 4.6 61.4 1.0
C S:SER84 4.7 28.0 1.0
C S:CYS85 4.8 29.5 1.0
CB S:ILE70 4.9 22.9 1.0
C S:ILE61 4.9 29.1 1.0
CG1 S:ILE70 4.9 20.6 1.0
N S:GLY86 4.9 29.8 1.0
OG S:SER84 4.9 33.1 1.0
CA S:SER84 4.9 27.1 1.0
N S:SER84 5.0 28.3 1.0

Reference:

K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa. Structures and Physiological Roles of 13 Integral Lipids of Bovine Heart Cytochrome C Oxidase Embo J. V. 26 1713 2007.
ISSN: ISSN 0261-4189
PubMed: 17332748
DOI: 10.1038/SJ.EMBOJ.7601618
Page generated: Wed Dec 16 03:22:25 2020

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