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Copper 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
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Sodium (Na) 4 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 6 binding sites of Copper 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 Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 6j8m

Go back to Copper Binding Sites List in 6j8m
Copper binding site 1 out of 6 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 Copper with other atoms in the Cu 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
A:Cu603

b:27.9
occ:1.00
 NE2 A:HIS291 2.0 23.8 1.0
ND1 A:HIS240 2.0 25.9 1.0
NE2 A:HIS290 2.0 28.2 1.0
O2 A:PER607 2.1 25.6 0.9
O2 A:PER607 2.3 15.0 0.1
O1 A:PER607 2.7 19.6 0.9
CE1 A:HIS291 2.9 23.8 1.0
CD2 A:HIS291 3.0 23.3 1.0
CE1 A:HIS240 3.0 24.3 1.0
CE1 A:HIS290 3.0 25.1 1.0
CG A:HIS240 3.0 25.4 1.0
CD2 A:HIS290 3.1 26.3 1.0
O1 A:PER607 3.1 15.1 0.1
CB A:HIS240 3.3 24.5 1.0
CA A:HIS240 3.9 23.6 1.0
ND1 A:HIS291 4.0 22.9 1.0
CG A:HIS291 4.1 22.9 1.0
NE2 A:HIS240 4.1 25.8 1.0
ND1 A:HIS290 4.1 24.4 1.0
CD2 A:HIS240 4.1 24.8 1.0
CG A:HIS290 4.2 24.7 1.0
C1A A:HEA602 4.5 25.5 1.0
NA A:HEA602 4.5 26.6 1.0
C4A A:HEA602 4.7 25.9 1.0
N A:HIS240 4.7 23.3 1.0
C2A A:HEA602 4.8 24.8 1.0
FE A:HEA602 4.8 27.7 1.0
CG2 A:VAL243 4.9 23.9 1.0
C3A A:HEA602 4.9 26.0 1.0
CHA A:HEA602 4.9 23.7 1.0

Copper binding site 2 out of 6 in 6j8m

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Copper binding site 2 out of 6 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 Copper with other atoms in the Cu 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
B:Cu302

b:30.4
occ:1.00
 CU1 B:CUA302 0.0 30.4 1.0
ND1 B:HIS161 2.1 25.3 1.0
SG B:CYS196 2.3 30.4 1.0
SG B:CYS200 2.3 27.9 1.0
SD B:MET207 2.4 31.4 1.0
CU2 B:CUA302 2.5 29.9 1.0
CE1 B:HIS161 3.0 25.2 1.0
CE B:MET207 3.1 28.9 1.0
CG B:HIS161 3.2 27.5 1.0
CB B:CYS200 3.3 27.5 1.0
CB B:CYS196 3.4 28.9 1.0
CG B:MET207 3.5 28.9 1.0
CB B:HIS161 3.6 27.3 1.0
O B:GLU198 4.0 28.7 1.0
NE2 B:HIS161 4.2 26.5 1.0
CA B:HIS161 4.2 27.8 1.0
CD2 B:HIS161 4.3 25.8 1.0
ND1 B:HIS204 4.4 29.0 1.0
O B:LEU160 4.6 27.8 1.0
O B:HIS102 4.7 29.1 1.0
CA B:CYS200 4.7 28.1 1.0
CA B:HIS204 4.7 27.9 1.0
CA B:CYS196 4.8 29.9 1.0
CD1 B:TRP104 4.8 27.6 1.0
CB B:MET207 4.8 30.1 1.0
O B:HIS204 4.9 27.2 1.0

Copper binding site 3 out of 6 in 6j8m

Go back to Copper Binding Sites List in 6j8m
Copper binding site 3 out of 6 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 Copper with other atoms in the Cu binding site number 3 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
B:Cu302

b:29.9
occ:1.00
 CU2 B:CUA302 0.0 29.9 1.0
ND1 B:HIS204 1.9 29.0 1.0
SG B:CYS200 2.3 27.9 1.0
SG B:CYS196 2.3 30.4 1.0
O B:GLU198 2.4 28.7 1.0
CU1 B:CUA302 2.5 30.4 1.0
CE1 B:HIS204 2.8 26.9 1.0
CG B:HIS204 3.1 28.5 1.0
CB B:CYS200 3.4 27.5 1.0
CB B:CYS196 3.4 28.9 1.0
C B:GLU198 3.5 29.8 1.0
CB B:HIS204 3.5 27.3 1.0
CA B:HIS204 3.6 27.9 1.0
O B:HIS204 3.7 27.2 1.0
N B:CYS200 3.7 28.6 1.0
NE2 B:HIS204 3.9 28.7 1.0
CD2 B:HIS204 4.1 28.4 1.0
C B:HIS204 4.1 27.1 1.0
N B:GLU198 4.1 28.3 1.0
C B:ILE199 4.1 28.3 1.0
O B:CYS196 4.1 26.8 1.0
C B:CYS196 4.2 31.1 1.0
CA B:CYS200 4.2 28.1 1.0
CA B:ILE199 4.2 28.7 1.0
N B:ILE199 4.2 28.3 1.0
ND1 B:HIS161 4.3 25.3 1.0
SD B:MET207 4.4 31.4 1.0
CA B:CYS196 4.4 29.9 1.0
CA B:GLU198 4.5 29.2 1.0
N B:SER197 4.6 28.3 1.0
CG B:MET207 4.6 28.9 1.0
N B:HIS204 4.9 26.7 1.0
CA B:HIS161 4.9 27.8 1.0
O B:ILE199 5.0 29.7 1.0

Copper binding site 4 out of 6 in 6j8m

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Copper binding site 4 out of 6 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 Copper with other atoms in the Cu binding site number 4 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
N:Cu603

b:29.4
occ:1.00
 ND1 N:HIS240 2.0 26.4 1.0
NE2 N:HIS291 2.0 26.9 1.0
O2 N:PER607 2.0 19.6 0.1
NE2 N:HIS290 2.0 29.9 1.0
O2 N:PER607 2.2 25.4 0.9
O1 N:PER607 2.8 21.5 0.9
CE1 N:HIS291 2.9 27.5 1.0
CE1 N:HIS290 3.0 28.6 1.0
CG N:HIS240 3.0 27.1 1.0
CE1 N:HIS240 3.0 26.3 1.0
CD2 N:HIS291 3.0 26.5 1.0
CD2 N:HIS290 3.0 27.6 1.0
O1 N:PER607 3.0 19.7 0.1
CB N:HIS240 3.3 26.8 1.0
CA N:HIS240 3.9 26.5 1.0
ND1 N:HIS291 4.0 27.5 1.0
CG N:HIS291 4.1 27.7 1.0
ND1 N:HIS290 4.1 28.6 1.0
NE2 N:HIS240 4.1 26.4 1.0
CD2 N:HIS240 4.1 27.0 1.0
CG N:HIS290 4.2 28.5 1.0
NA N:HEA602 4.5 28.9 1.0
C1A N:HEA602 4.6 28.2 1.0
C4A N:HEA602 4.7 27.9 1.0
N N:HIS240 4.7 25.9 1.0
FE N:HEA602 4.8 29.2 1.0
C2A N:HEA602 4.8 27.9 1.0
C3A N:HEA602 4.9 28.1 1.0
CG2 N:VAL243 5.0 26.3 1.0
CHA N:HEA602 5.0 27.5 1.0

Copper binding site 5 out of 6 in 6j8m

Go back to Copper Binding Sites List in 6j8m
Copper binding site 5 out of 6 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 Copper with other atoms in the Cu binding site number 5 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
O:Cu302

b:34.9
occ:1.00
 CU1 O:CUA302 0.0 34.9 1.0
ND1 O:HIS161 2.1 33.4 1.0
SG O:CYS196 2.3 35.2 1.0
SG O:CYS200 2.3 34.2 1.0
SD O:MET207 2.3 37.3 1.0
CU2 O:CUA302 2.6 35.0 1.0
CE1 O:HIS161 3.0 32.2 1.0
CE O:MET207 3.0 33.3 1.0
CG O:HIS161 3.2 33.3 1.0
CB O:CYS200 3.3 33.3 1.0
CB O:CYS196 3.4 35.0 1.0
CG O:MET207 3.5 35.3 1.0
CB O:HIS161 3.6 32.7 1.0
O O:GLU198 4.1 31.2 1.0
NE2 O:HIS161 4.1 34.2 1.0
CA O:HIS161 4.2 34.5 1.0
CD2 O:HIS161 4.3 33.0 1.0
ND1 O:HIS204 4.5 31.2 1.0
O O:LEU160 4.6 33.1 1.0
O O:HIS102 4.7 34.6 1.0
CA O:CYS200 4.7 32.7 1.0
CD1 O:TRP104 4.7 33.7 1.0
CA O:HIS204 4.7 33.0 1.0
CA O:CYS196 4.7 35.0 1.0
CB O:MET207 4.9 34.9 1.0
O O:HIS204 4.9 30.8 1.0

Copper binding site 6 out of 6 in 6j8m

Go back to Copper Binding Sites List in 6j8m
Copper binding site 6 out of 6 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 Copper with other atoms in the Cu binding site number 6 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
O:Cu302

b:35.0
occ:1.00
 CU2 O:CUA302 0.0 35.0 1.0
ND1 O:HIS204 2.0 31.2 1.0
SG O:CYS200 2.2 34.2 1.0
SG O:CYS196 2.3 35.2 1.0
O O:GLU198 2.4 31.2 1.0
CU1 O:CUA302 2.6 34.9 1.0
CE1 O:HIS204 2.8 30.2 1.0
CG O:HIS204 3.1 31.2 1.0
CB O:CYS200 3.3 33.3 1.0
CB O:CYS196 3.3 35.0 1.0
C O:GLU198 3.5 31.6 1.0
CB O:HIS204 3.6 32.8 1.0
CA O:HIS204 3.6 33.0 1.0
N O:CYS200 3.7 32.2 1.0
O O:HIS204 3.8 30.8 1.0
NE2 O:HIS204 4.0 30.9 1.0
N O:GLU198 4.1 32.2 1.0
C O:ILE199 4.1 32.9 1.0
CA O:CYS200 4.1 32.7 1.0
CD2 O:HIS204 4.1 32.2 1.0
C O:HIS204 4.1 33.4 1.0
N O:ILE199 4.2 30.9 1.0
CA O:ILE199 4.2 31.5 1.0
C O:CYS196 4.2 34.9 1.0
O O:CYS196 4.2 32.9 1.0
ND1 O:HIS161 4.3 33.4 1.0
SD O:MET207 4.4 37.3 1.0
CA O:CYS196 4.4 35.0 1.0
CA O:GLU198 4.5 31.9 1.0
N O:SER197 4.6 34.6 1.0
CG O:MET207 4.7 35.3 1.0
N O:HIS204 4.8 34.1 1.0
O O:ILE199 4.9 32.9 1.0
CA O:HIS161 5.0 34.5 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: Wed Jul 31 06:19:24 2024

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