Atomistry » Copper » PDB 2z7y-3aws » 3abm
Atomistry »
  Copper »
    PDB 2z7y-3aws »
      3abm »

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

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 3abm

Go back to Copper Binding Sites List in 3abm
Copper binding site 1 out of 6 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 Copper with other atoms in the Cu 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
A:Cu517

b:29.1
occ:1.00
 NE2 A:HIS291 2.0 30.6 1.0
ND1 A:HIS240 2.1 30.7 1.0
NE2 A:HIS290 2.1 24.4 1.0
O2 A:PER520 2.2 32.9 1.0
O1 A:PER520 2.8 25.6 1.0
CD2 A:HIS291 2.9 25.8 1.0
CE1 A:HIS291 3.0 25.2 1.0
CD2 A:HIS290 3.0 24.2 1.0
CE1 A:HIS240 3.1 27.7 1.0
CG A:HIS240 3.1 29.1 1.0
CE1 A:HIS290 3.2 27.5 1.0
CB A:HIS240 3.4 27.9 1.0
CA A:HIS240 3.9 25.5 1.0
CG A:HIS291 4.1 27.6 1.0
ND1 A:HIS291 4.1 23.9 1.0
NE2 A:HIS240 4.2 29.9 1.0
CD2 A:HIS240 4.2 27.7 1.0
CG A:HIS290 4.2 29.9 1.0
ND1 A:HIS290 4.2 27.5 1.0
NA A:HEA516 4.5 22.3 1.0
C1A A:HEA516 4.6 23.8 1.0
C4A A:HEA516 4.7 20.9 1.0
N A:HIS240 4.8 25.3 1.0
C2A A:HEA516 4.8 21.2 1.0
CG2 A:VAL243 4.9 27.0 1.0
FE A:HEA516 4.9 27.1 1.0
CHA A:HEA516 4.9 23.4 1.0
ND A:HEA516 5.0 26.8 1.0

Copper binding site 2 out of 6 in 3abm

Go back to Copper Binding Sites List in 3abm
Copper binding site 2 out of 6 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 Copper with other atoms in the Cu 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
B:Cu228

b:30.0
occ:1.00
 CU1 B:CUA228 0.0 30.0 1.0
ND1 B:HIS161 2.0 26.8 1.0
SG B:CYS196 2.3 27.4 1.0
SG B:CYS200 2.4 26.4 1.0
SD B:MET207 2.4 28.1 1.0
CU2 B:CUA228 2.5 27.4 1.0
CE1 B:HIS161 2.9 20.0 1.0
CE B:MET207 3.1 22.4 1.0
CG B:HIS161 3.1 26.1 1.0
CB B:CYS196 3.4 23.0 1.0
CB B:CYS200 3.4 31.1 1.0
CG B:MET207 3.5 24.9 1.0
CB B:HIS161 3.6 24.7 1.0
O B:GLU198 4.0 29.4 1.0
NE2 B:HIS161 4.1 23.9 1.0
CD2 B:HIS161 4.2 20.6 1.0
CA B:HIS161 4.2 24.4 1.0
ND1 B:HIS204 4.5 30.2 1.0
O B:LEU160 4.6 27.1 1.0
CD1 B:TRP104 4.7 21.3 1.0
CA B:HIS204 4.7 28.1 1.0
O B:HIS102 4.7 28.4 1.0
CA B:CYS196 4.8 24.6 1.0
CA B:CYS200 4.8 28.2 1.0
O B:HIS204 4.9 28.3 1.0
CB B:MET207 4.9 27.5 1.0

Copper binding site 3 out of 6 in 3abm

Go back to Copper Binding Sites List in 3abm
Copper binding site 3 out of 6 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 Copper with other atoms in the Cu binding site number 3 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
B:Cu228

b:27.4
occ:1.00
 CU2 B:CUA228 0.0 27.4 1.0
ND1 B:HIS204 2.0 30.2 1.0
O B:GLU198 2.2 29.4 1.0
SG B:CYS200 2.2 26.4 1.0
SG B:CYS196 2.3 27.4 1.0
CU1 B:CUA228 2.5 30.0 1.0
CE1 B:HIS204 2.9 29.4 1.0
CG B:HIS204 3.1 27.4 1.0
CB B:CYS196 3.3 23.0 1.0
C B:GLU198 3.4 27.3 1.0
CB B:HIS204 3.6 26.6 1.0
CB B:CYS200 3.6 31.1 1.0
CA B:HIS204 3.6 28.1 1.0
N B:CYS200 3.8 28.7 1.0
O B:HIS204 3.8 28.3 1.0
NE2 B:HIS204 4.1 27.9 1.0
N B:GLU198 4.1 25.0 1.0
ND1 B:HIS161 4.2 26.8 1.0
C B:HIS204 4.2 26.8 1.0
C B:ILE199 4.2 27.2 1.0
CD2 B:HIS204 4.2 27.5 1.0
C B:CYS196 4.2 26.2 1.0
N B:ILE199 4.2 29.3 1.0
CA B:ILE199 4.3 25.0 1.0
O B:CYS196 4.3 23.7 1.0
CA B:CYS200 4.3 28.2 1.0
SD B:MET207 4.4 28.1 1.0
CA B:CYS196 4.4 24.6 1.0
CA B:GLU198 4.4 27.0 1.0
N B:SER197 4.6 25.5 1.0
CG B:MET207 4.7 24.9 1.0
CA B:HIS161 4.9 24.4 1.0
N B:HIS204 4.9 27.0 1.0
CE1 B:HIS161 5.0 20.0 1.0

Copper binding site 4 out of 6 in 3abm

Go back to Copper Binding Sites List in 3abm
Copper binding site 4 out of 6 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 Copper with other atoms in the Cu binding site number 4 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
N:Cu517

b:32.4
occ:1.00
 NE2 N:HIS290 2.0 30.5 1.0
NE2 N:HIS291 2.0 34.4 1.0
ND1 N:HIS240 2.1 30.6 1.0
O2 N:PER520 2.1 35.0 1.0
O1 N:PER520 2.6 31.0 1.0
CE1 N:HIS290 3.0 32.3 1.0
CG N:HIS240 3.0 32.4 1.0
CE1 N:HIS291 3.0 29.3 1.0
CD2 N:HIS291 3.0 28.7 1.0
CD2 N:HIS290 3.1 28.9 1.0
CE1 N:HIS240 3.1 29.4 1.0
CB N:HIS240 3.3 34.1 1.0
CA N:HIS240 3.8 33.1 1.0
ND1 N:HIS290 4.1 31.2 1.0
ND1 N:HIS291 4.1 26.4 1.0
CG N:HIS291 4.1 34.4 1.0
CD2 N:HIS240 4.2 26.4 1.0
CG N:HIS290 4.2 32.0 1.0
NE2 N:HIS240 4.2 33.0 1.0
NA N:HEA516 4.5 31.2 1.0
C1A N:HEA516 4.6 28.9 1.0
N N:HIS240 4.7 31.7 1.0
C4A N:HEA516 4.7 28.3 1.0
CG2 N:VAL243 4.7 33.3 1.0
FE N:HEA516 4.9 33.7 1.0
CHA N:HEA516 4.9 30.2 1.0
C2A N:HEA516 4.9 27.6 1.0
ND N:HEA516 4.9 33.8 1.0

Copper binding site 5 out of 6 in 3abm

Go back to Copper Binding Sites List in 3abm
Copper binding site 5 out of 6 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 Copper with other atoms in the Cu binding site number 5 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
O:Cu228

b:37.8
occ:1.00
 CU1 O:CUA228 0.0 37.8 1.0
ND1 O:HIS161 2.0 32.9 1.0
SG O:CYS200 2.3 35.2 1.0
SG O:CYS196 2.3 36.3 1.0
SD O:MET207 2.4 37.5 1.0
CE1 O:HIS161 2.5 31.8 1.0
CU2 O:CUA228 2.6 36.9 1.0
CE O:MET207 3.1 30.6 1.0
CG O:HIS161 3.3 31.2 1.0
CB O:CYS200 3.4 33.7 1.0
CB O:CYS196 3.5 32.4 1.0
CG O:MET207 3.6 33.8 1.0
NE2 O:HIS161 3.8 29.8 1.0
CB O:HIS161 3.9 33.8 1.0
O O:GLU198 4.0 35.6 1.0
CD2 O:HIS161 4.1 30.1 1.0
CA O:HIS161 4.3 34.6 1.0
ND1 O:HIS204 4.5 36.6 1.0
CD1 O:TRP104 4.6 36.1 1.0
O O:LEU160 4.7 30.4 1.0
CA O:HIS204 4.8 34.4 1.0
CA O:CYS200 4.8 33.1 1.0
O O:HIS102 4.8 36.6 1.0
O O:HIS204 4.8 34.6 1.0
CA O:CYS196 4.8 33.6 1.0
CB O:MET207 4.9 33.5 1.0

Copper binding site 6 out of 6 in 3abm

Go back to Copper Binding Sites List in 3abm
Copper binding site 6 out of 6 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 Copper with other atoms in the Cu binding site number 6 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
O:Cu228

b:36.9
occ:1.00
 CU2 O:CUA228 0.0 36.9 1.0
ND1 O:HIS204 2.0 36.6 1.0
O O:GLU198 2.1 35.6 1.0
SG O:CYS200 2.3 35.2 1.0
SG O:CYS196 2.3 36.3 1.0
CU1 O:CUA228 2.6 37.8 1.0
CE1 O:HIS204 2.9 38.1 1.0
CG O:HIS204 3.1 35.2 1.0
CB O:CYS196 3.4 32.4 1.0
C O:GLU198 3.4 30.9 1.0
CB O:CYS200 3.5 33.7 1.0
CB O:HIS204 3.6 35.1 1.0
CA O:HIS204 3.7 34.4 1.0
O O:HIS204 3.7 34.6 1.0
N O:CYS200 3.8 33.0 1.0
NE2 O:HIS204 4.1 28.4 1.0
ND1 O:HIS161 4.1 32.9 1.0
N O:GLU198 4.1 30.0 1.0
C O:HIS204 4.2 33.4 1.0
CD2 O:HIS204 4.2 31.2 1.0
C O:ILE199 4.2 32.1 1.0
C O:CYS196 4.2 34.0 1.0
O O:CYS196 4.2 31.5 1.0
CA O:CYS200 4.3 33.1 1.0
N O:ILE199 4.3 30.8 1.0
CA O:ILE199 4.3 31.6 1.0
SD O:MET207 4.4 37.5 1.0
CA O:GLU198 4.4 31.0 1.0
CA O:CYS196 4.5 33.6 1.0
N O:SER197 4.6 31.7 1.0
CE1 O:HIS161 4.7 31.8 1.0
CG O:MET207 4.8 33.8 1.0
N O:HIS204 4.9 36.0 1.0
O O:ILE199 5.0 31.3 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 Jul 31 00:35:20 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy