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Zinc in PDB 5iy5: Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution

Enzymatic activity of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution

All present enzymatic activity of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution, PDB code: 5iy5 was solved by S.Shimada, J.Baba, S.Aoe, A.Shimada, E.Yamashita, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.290, 183.872, 148.929, 90.00, 102.12, 90.00
R / Rfree (%) 16.7 / 20.7

Other elements in 5iy5:

The structure of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution (pdb code 5iy5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution, PDB code: 5iy5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5iy5

Go back to Zinc Binding Sites List in 5iy5
Zinc binding site 1 out of 2 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:36.3
occ:1.00
SG F:CYS60 2.3 35.2 1.0
SG F:CYS82 2.4 35.9 1.0
SG F:CYS85 2.4 34.7 1.0
SG F:CYS62 2.4 36.1 1.0
CB F:CYS82 3.1 35.0 1.0
CB F:CYS60 3.3 31.9 1.0
CB F:CYS62 3.4 33.5 1.0
CB F:CYS85 3.4 32.9 1.0
N F:CYS85 3.6 35.5 1.0
CA F:CYS62 3.7 35.8 1.0
CA F:CYS85 4.1 33.5 1.0
N F:CYS62 4.2 33.0 1.0
O F:CYS60 4.4 35.4 1.0
CA F:CYS60 4.5 31.8 1.0
CB F:SER84 4.5 34.9 1.0
C F:CYS60 4.5 33.5 1.0
CA F:CYS82 4.6 36.7 1.0
C F:SER84 4.6 34.3 1.0
CG2 F:THR87 4.6 37.9 1.0
OG F:SER84 4.7 39.4 1.0
C F:CYS85 4.8 34.8 1.0
O F:HOH237 4.8 51.6 1.0
CB F:ILE70 4.9 31.2 1.0
CA F:SER84 4.9 33.7 1.0
N F:SER84 4.9 37.2 1.0
N F:GLY86 4.9 32.9 1.0
C F:ILE61 5.0 37.4 1.0

Zinc binding site 2 out of 2 in 5iy5

Go back to Zinc Binding Sites List in 5iy5
Zinc binding site 2 out of 2 in the Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Electron Transfer Complex of Cytochrome C and Cytochrome C Oxidase at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:37.8
occ:1.00
SG S:CYS60 1.9 40.4 1.0
SG S:CYS85 2.1 38.6 1.0
SG S:CYS82 2.2 38.9 1.0
SG S:CYS62 2.4 41.0 1.0
CB S:CYS82 3.1 41.4 1.0
CB S:CYS60 3.1 41.5 1.0
CB S:CYS85 3.2 35.3 1.0
CB S:CYS62 3.4 41.9 1.0
N S:CYS85 3.6 40.4 1.0
CA S:CYS62 3.7 44.5 1.0
CA S:CYS85 4.0 42.3 1.0
N S:CYS62 4.3 46.0 1.0
CA S:CYS60 4.4 40.5 1.0
OG S:SER84 4.4 40.4 1.0
C S:CYS60 4.4 34.7 1.0
O S:CYS60 4.4 36.6 1.0
CB S:SER84 4.5 40.9 1.0
C S:SER84 4.6 38.8 1.0
CA S:CYS82 4.6 46.8 1.0
O S:HOH258 4.6 56.0 1.0
N S:GLY86 4.7 43.4 1.0
CG2 S:THR87 4.7 46.0 1.0
C S:CYS85 4.8 42.3 1.0
CA S:SER84 4.9 36.7 1.0
CB S:ILE70 4.9 34.8 1.0
C S:ILE61 4.9 40.4 1.0
CG1 S:ILE70 4.9 34.7 1.0
N S:SER84 4.9 39.1 1.0
C S:CYS62 5.0 47.3 1.0

Reference:

S.Shimada, K.Shinzawa-Itoh, J.Baba, S.Aoe, A.Shimada, E.Yamashita, J.Kang, M.Tateno, S.Yoshikawa, T.Tsukihara. Complex Structure of Cytochrome C-Cytochrome C Oxidase Reveals A Novel Protein-Protein Interaction Mode Embo J. V. 36 291 2017.
ISSN: ESSN 1460-2075
PubMed: 27979921
DOI: 10.15252/EMBJ.201695021
Page generated: Wed Dec 16 06:23:02 2020

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