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Copper in PDB 5z86: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days
Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days
All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days:
1.9.3.1;
1.9.3.1;
Protein crystallography data
The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days, PDB code: 5z86
was solved by
A.Shimada,
K.Hatano,
H.Tadehara,
T.Tsukihara,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
| Resolution Low / High (Å) | 40.00 / 1.85 |
| Space group | P 21 21 21 |
| Cell size a, b, c (Å), α, β, γ (°) | 183.490, 206.292, 177.617, 90.00, 90.00, 90.00 |
| R / Rfree (%) | 18.1 / 19.6 |
Other elements in 5z86:
The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days also contains other interesting chemical elements:
| Magnesium | (Mg) | 2 atoms |
| Zinc | (Zn) | 2 atoms |
| Iron | (Fe) | 6 atoms |
| Sodium | (Na) | 2 atoms |
Copper Binding Sites:
The binding sites of Copper atom in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days
(pdb code 5z86). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days, PDB code: 5z86:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;
In total 6 binding sites of Copper where determined in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days, PDB code: 5z86:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;
Copper binding site 1 out of 6 in 5z86
Go back to
Copper Binding Sites List in 5z86
Copper binding site 1 out
of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days within 5.0Å range:
|
Copper binding site 2 out of 6 in 5z86
Go back to
Copper Binding Sites List in 5z86
Copper binding site 2 out
of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days within 5.0Å range:
|
Copper binding site 3 out of 6 in 5z86
Go back to
Copper Binding Sites List in 5z86
Copper binding site 3 out
of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days within 5.0Å range:
|
Copper binding site 4 out of 6 in 5z86
Go back to
Copper Binding Sites List in 5z86
Copper binding site 4 out
of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days within 5.0Å range:
|
Copper binding site 5 out of 6 in 5z86
Go back to
Copper Binding Sites List in 5z86
Copper binding site 5 out
of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days within 5.0Å range:
|
Copper binding site 6 out of 6 in 5z86
Go back to
Copper Binding Sites List in 5z86
Copper binding site 6 out
of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 3 Days within 5.0Å range:
|
Reference:
A.Shimada,
K.Hatano,
H.Tadehara,
N.Yano,
K.Shinzawa-Itoh,
E.Yamashita,
K.Muramoto,
T.Tsukihara,
S.Yoshikawa.
X-Ray Structural Analyses of Azide-Bound Cytochromecoxidases Reveal That the H-Pathway Is Critically Important For the Proton-Pumping Activity. J. Biol. Chem. V. 293 14868 2018.
ISSN: ESSN 1083-351X
PubMed: 30077971
DOI: 10.1074/JBC.RA118.003123
Page generated: Mon Jul 14 05:44:32 2025
ISSN: ESSN 1083-351X
PubMed: 30077971
DOI: 10.1074/JBC.RA118.003123
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