Atomistry » Copper » PDB 6ied-6l58 » 6j8m
Atomistry »
  Copper »
    PDB 6ied-6l58 »
      6j8m »

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

Go back to Copper Binding Sites List in 6j8m
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

Go back to Copper Binding Sites List in 6j8m
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy