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Zinc in PDB 6j8m: Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray

Enzymatic activity of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray

All present enzymatic activity of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray:
1.9.3.1;

Protein crystallography data

The structure of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray, PDB code: 6j8m was solved by G.Ueno, A.Shimada, E.Yamashita, K.Hasegawa, T.Kumasaka, K.Shinzawa-Itoh, S.Yoshikawa, T.Tsukihara, M.Yamamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.020, 203.540, 177.410, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.9

Other elements in 6j8m:

The structure of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray (pdb code 6j8m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray, PDB code: 6j8m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6j8m

Go back to Zinc Binding Sites List in 6j8m
Zinc binding site 1 out of 2 in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:33.1
occ:1.00
 SG F:CYS62 2.3 32.6 1.0
SG F:CYS60 2.3 34.3 1.0
SG F:CYS82 2.3 30.9 1.0
SG F:CYS85 2.4 34.1 1.0
CB F:CYS82 3.1 31.4 1.0
CB F:CYS60 3.3 32.5 1.0
CB F:CYS62 3.3 32.5 1.0
CB F:CYS85 3.3 31.9 1.0
CA F:CYS62 3.6 36.3 1.0
N F:CYS85 3.7 34.2 1.0
CA F:CYS85 4.1 32.8 1.0
N F:CYS62 4.1 34.2 1.0
O F:CYS60 4.3 31.0 1.0
C F:CYS60 4.4 32.4 1.0
CA F:CYS60 4.4 30.5 1.0
O F:HOH226 4.5 48.9 1.0
CA F:CYS82 4.6 32.0 1.0
CB F:SER84 4.6 32.2 1.0
OG F:SER84 4.6 34.2 1.0
C F:SER84 4.7 33.8 1.0
C F:CYS85 4.8 34.4 1.0
CG2 F:THR87 4.9 42.9 1.0
C F:ILE61 4.9 36.1 1.0
CB F:ILE70 4.9 30.2 1.0
OG1 F:THR87 4.9 50.6 1.0
C F:CYS62 4.9 38.6 1.0
N F:GLY86 4.9 32.7 1.0
CG1 F:ILE70 5.0 30.1 1.0
N F:SER84 5.0 34.6 1.0

Zinc binding site 2 out of 2 in 6j8m

Go back to Zinc Binding Sites List in 6j8m
Zinc binding site 2 out of 2 in the Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Low-Dose Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Determined Using 30 Kev X-Ray within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:34.3
occ:1.00
 SG S:CYS82 2.3 33.4 1.0
SG S:CYS62 2.3 35.4 1.0
SG S:CYS60 2.4 32.6 1.0
SG S:CYS85 2.4 33.7 1.0
CB S:CYS82 3.1 32.1 1.0
CB S:CYS60 3.2 31.9 1.0
CB S:CYS62 3.3 33.2 1.0
CB S:CYS85 3.4 33.5 1.0
CA S:CYS62 3.6 34.1 1.0
N S:CYS85 3.7 34.1 1.0
N S:CYS62 4.1 34.8 1.0
CG2 S:THR87 4.1 37.2 0.5
CA S:CYS85 4.1 34.0 1.0
C S:CYS60 4.4 32.9 1.0
O S:CYS60 4.4 29.8 1.0
CA S:CYS60 4.4 30.2 1.0
O S:HOH215 4.4 44.5 1.0
CB S:SER84 4.5 35.4 1.0
CG2 S:THR87 4.6 35.0 0.5
CA S:CYS82 4.6 33.4 1.0
OG S:SER84 4.7 38.8 1.0
C S:SER84 4.7 34.6 1.0
C S:ILE61 4.8 34.8 1.0
C S:CYS85 4.9 36.3 1.0
N S:GLY86 4.9 35.1 1.0
OG1 S:THR87 4.9 37.0 0.5
C S:CYS62 5.0 39.3 1.0
CB S:ILE70 5.0 30.6 1.0
CA S:SER84 5.0 35.4 1.0

Reference:

G.Ueno, A.Shimada, E.Yamashita, K.Hasegawa, T.Kumasaka, K.Shinzawa-Itoh, S.Yoshikawa, T.Tsukihara, M.Yamamoto. Low-Dose X-Ray Structure Analysis of Cytochrome C Oxidase Utilizing High-Energy X-Rays. J.Synchrotron Radiat. V. 26 912 2019.
ISSN: ESSN 1600-5775
PubMed: 31274413
DOI: 10.1107/S1600577519006805
Page generated: Tue Oct 29 00:57:08 2024

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