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Zinc in PDB 2eik: Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

Enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

All present enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State:
1.9.3.1;

Protein crystallography data

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik was solved by K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, 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 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.321, 206.525, 178.159, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 22.8

Other elements in 2eik:

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 2eik). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2eik

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

b:24.1
occ:1.00
SG F:CYS62 2.2 29.2 1.0
SG F:CYS60 2.3 29.8 1.0
SG F:CYS85 2.3 31.6 1.0
SG F:CYS82 2.3 25.7 1.0
CB F:CYS82 3.2 27.7 1.0
CB F:CYS62 3.3 26.5 1.0
CB F:CYS60 3.4 25.2 1.0
CB F:CYS85 3.4 28.8 1.0
CA F:CYS62 3.5 33.3 1.0
N F:CYS85 3.6 30.1 1.0
N F:CYS62 3.8 30.9 1.0
CA F:CYS85 4.1 31.0 1.0
O F:CYS60 4.3 26.8 1.0
O F:HOH2339 4.3 48.2 1.0
C F:CYS60 4.4 24.5 1.0
CB F:SER84 4.5 28.0 1.0
CA F:CYS60 4.5 22.7 1.0
OG F:SER84 4.6 28.4 1.0
CA F:CYS82 4.7 25.7 1.0
C F:SER84 4.7 28.7 1.0
CG1 F:ILE70 4.8 19.9 1.0
C F:ILE61 4.8 29.0 1.0
C F:CYS85 4.8 32.6 1.0
C F:CYS62 4.9 38.6 1.0
OG1 F:THR87 4.9 42.6 1.0
CB F:ILE70 4.9 23.0 1.0
CA F:SER84 5.0 27.3 1.0
N F:GLY86 5.0 34.6 1.0

Zinc binding site 2 out of 2 in 2eik

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

b:29.4
occ:1.00
SG S:CYS85 2.2 34.6 1.0
SG S:CYS62 2.2 32.9 1.0
SG S:CYS82 2.2 31.0 1.0
SG S:CYS60 2.3 32.9 1.0
CB S:CYS82 3.0 29.9 1.0
CB S:CYS60 3.3 28.7 1.0
CB S:CYS85 3.4 31.3 1.0
CB S:CYS62 3.4 35.1 1.0
N S:CYS85 3.6 31.8 1.0
CA S:CYS62 3.7 37.1 1.0
N S:CYS62 4.0 36.0 1.0
CA S:CYS85 4.1 32.2 1.0
OG1 S:THR87 4.3 41.5 1.0
O N:HOH3339 4.4 64.3 1.0
O S:CYS60 4.4 29.2 1.0
C S:CYS60 4.4 29.0 1.0
CA S:CYS60 4.5 30.0 1.0
CA S:CYS82 4.5 32.2 1.0
CB S:SER84 4.5 36.5 1.0
NZ N:LYS514 4.7 74.4 1.0
C S:SER84 4.7 33.0 1.0
C S:CYS85 4.8 31.3 1.0
CB S:ILE70 4.8 26.1 1.0
CG1 S:ILE70 4.8 24.3 1.0
N S:GLY86 4.9 33.6 1.0
N S:SER84 4.9 34.7 1.0
CA S:SER84 4.9 33.6 1.0
C S:ILE61 4.9 35.4 1.0

Reference:

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa. A Histidine Residue Acting As A Controlling Site For Dioxygen Reduction and Proton Pumping By Cytochrome C Oxidase Proc.Natl.Acad.Sci.Usa V. 104 7881 2007.
ISSN: ISSN 0027-8424
PubMed: 17470809
DOI: 10.1073/PNAS.0610031104
Page generated: Wed Dec 16 03:24:27 2020

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