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Zinc in PDB 3abm: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset), PDB code: 3abm was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.697, 206.991, 178.251, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.4

Other elements in 3abm:

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset) 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 (200-S X-Ray Exposure Dataset) (pdb code 3abm). 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 (200-S X-Ray Exposure Dataset), PDB code: 3abm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3abm

Go back to Zinc Binding Sites List in 3abm
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)


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 (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn99

b:34.3
occ:1.00
SG F:CYS82 2.3 32.2 1.0
SG F:CYS60 2.3 34.5 1.0
SG F:CYS62 2.3 34.1 1.0
SG F:CYS85 2.4 36.8 1.0
CB F:CYS82 3.2 31.7 1.0
CB F:CYS60 3.2 32.6 1.0
CB F:CYS62 3.4 33.8 1.0
CB F:CYS85 3.5 31.8 1.0
CA F:CYS62 3.6 36.8 1.0
N F:CYS85 3.8 34.0 1.0
N F:CYS62 4.1 37.5 1.0
CA F:CYS85 4.2 33.2 1.0
O F:CYS60 4.4 33.8 1.0
C F:CYS60 4.4 32.0 1.0
CA F:CYS60 4.4 31.0 1.0
CA F:CYS82 4.6 31.7 1.0
O F:HOH2332 4.6 47.2 1.0
OG F:SER84 4.7 38.5 1.0
CB F:SER84 4.8 37.2 1.0
C F:SER84 4.8 34.5 1.0
CB F:ILE70 4.8 30.5 1.0
C F:ILE61 4.8 36.4 1.0
C F:CYS85 4.9 36.3 1.0
CG1 F:ILE70 4.9 29.6 1.0
OG1 F:THR87 4.9 44.8 1.0
C F:CYS62 5.0 38.8 1.0
CG2 F:THR87 5.0 39.3 1.0

Zinc binding site 2 out of 2 in 3abm

Go back to Zinc Binding Sites List in 3abm
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)


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 (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn99

b:39.0
occ:1.00
SG S:CYS82 2.3 38.1 1.0
SG S:CYS85 2.4 36.4 1.0
SG S:CYS62 2.4 38.6 1.0
SG S:CYS60 2.4 37.4 1.0
CB S:CYS82 3.1 35.5 1.0
CB S:CYS60 3.3 34.5 1.0
CB S:CYS62 3.4 39.4 1.0
CB S:CYS85 3.5 34.1 1.0
CA S:CYS62 3.6 39.7 1.0
N S:CYS85 3.7 35.7 1.0
N S:CYS62 4.0 40.1 1.0
CA S:CYS85 4.2 35.2 1.0
O S:CYS60 4.4 38.7 1.0
C S:CYS60 4.4 36.6 1.0
CA S:CYS60 4.5 36.0 1.0
CB S:SER84 4.5 38.3 1.0
CA S:CYS82 4.5 36.2 1.0
O S:HOH3332 4.6 52.3 1.0
C S:SER84 4.7 37.4 1.0
OG S:SER84 4.7 38.9 1.0
C S:ILE61 4.8 40.2 1.0
CG2 S:THR87 4.8 42.1 1.0
C S:CYS85 4.8 36.6 1.0
CA S:SER84 4.9 38.4 1.0
N S:SER84 4.9 39.5 1.0
CB S:ILE70 4.9 32.7 1.0
CG1 S:ILE70 4.9 33.6 1.0
N S:GLY86 5.0 39.7 1.0
C S:CYS62 5.0 40.8 1.0
N S:ILE61 5.0 36.6 1.0

Reference:

H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa. A Peroxide Bridge Between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump Proc.Natl.Acad.Sci.Usa V. 106 2165 2009.
ISSN: ISSN 0027-8424
PubMed: 19164527
DOI: 10.1073/PNAS.0806391106
Page generated: Wed Dec 16 04:06:42 2020

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