Atomistry » Copper » PDB 2z7y-3aws » 3ag4
Atomistry »
  Copper »
    PDB 2z7y-3aws »
      3ag4 »

Copper in PDB 3ag4: Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4 was solved by K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.364, 206.648, 178.137, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.9

Other elements in 3ag4:

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K 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 in the Cyanide Ion-Bound Fully Reduced State at 100 K (pdb code 3ag4). 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 in the Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 in the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:31.0
occ:1.00
ND1 A:HIS240 2.0 33.7 1.0
NE2 A:HIS291 2.0 34.0 1.0
N A:CYN520 2.3 31.4 1.0
NE2 A:HIS290 2.8 36.2 1.0
C A:CYN520 2.9 31.3 1.0
CE1 A:HIS240 2.9 25.0 1.0
CE1 A:HIS291 3.0 27.5 1.0
CG A:HIS240 3.0 27.9 1.0
CD2 A:HIS291 3.0 28.4 1.0
CB A:HIS240 3.4 25.4 1.0
CE1 A:HIS290 3.7 31.7 1.0
CD2 A:HIS290 3.7 36.8 1.0
CA A:HIS240 3.8 23.6 1.0
NE2 A:HIS240 4.0 27.1 1.0
CD2 A:HIS240 4.1 27.3 1.0
ND1 A:HIS291 4.1 28.3 1.0
CG A:HIS291 4.2 30.4 1.0
CG2 A:VAL243 4.4 27.0 1.0
N A:HIS240 4.7 24.3 1.0
O A:HOH4310 4.7 38.4 1.0
ND1 A:HIS290 4.8 35.5 1.0
CG A:HIS290 4.9 32.7 1.0
C A:HIS240 4.9 25.6 1.0
ND A:HEA516 4.9 27.7 1.0
C1A A:HEA516 4.9 29.1 1.0
O A:HIS240 4.9 27.0 1.0
NA A:HEA516 4.9 30.2 1.0
FE A:HEA516 5.0 35.5 1.0
CZ3 A:TRP236 5.0 29.3 1.0

Copper binding site 2 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 in the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:28.4
occ:1.00
CU1 B:CUA228 0.0 28.4 1.0
ND1 B:HIS161 2.0 19.6 1.0
SD B:MET207 2.4 29.0 1.0
SG B:CYS200 2.4 29.1 1.0
SG B:CYS196 2.4 27.6 1.0
CU2 B:CUA228 2.5 28.8 1.0
CE1 B:HIS161 2.9 24.8 1.0
CE B:MET207 3.0 20.4 1.0
CG B:HIS161 3.1 24.5 1.0
CB B:CYS200 3.3 28.6 1.0
CB B:CYS196 3.5 24.7 1.0
CG B:MET207 3.5 26.4 1.0
CB B:HIS161 3.6 25.2 1.0
O B:GLU198 4.0 32.0 1.0
NE2 B:HIS161 4.0 23.2 1.0
CD2 B:HIS161 4.2 22.4 1.0
CA B:HIS161 4.2 25.5 1.0
ND1 B:HIS204 4.5 28.6 1.0
CD1 B:TRP104 4.5 25.6 1.0
O B:HIS102 4.6 26.8 1.0
CA B:HIS204 4.7 28.0 1.0
O B:LEU160 4.8 26.1 1.0
CA B:CYS200 4.8 27.9 1.0
CB B:MET207 4.8 27.5 1.0
CA B:CYS196 4.9 27.1 1.0
O B:HIS204 5.0 26.6 1.0
CZ2 B:TRP106 5.0 27.3 1.0

Copper binding site 3 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 in the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:28.8
occ:1.00
CU2 B:CUA228 0.0 28.8 1.0
ND1 B:HIS204 2.0 28.6 1.0
SG B:CYS196 2.3 27.6 1.0
SG B:CYS200 2.3 29.1 1.0
O B:GLU198 2.3 32.0 1.0
CU1 B:CUA228 2.5 28.4 1.0
CE1 B:HIS204 2.9 26.7 1.0
CG B:HIS204 3.2 28.1 1.0
CB B:CYS196 3.3 24.7 1.0
CA B:HIS204 3.5 28.0 1.0
CB B:CYS200 3.5 28.6 1.0
C B:GLU198 3.6 29.9 1.0
CB B:HIS204 3.6 26.3 1.0
N B:CYS200 3.7 26.9 1.0
O B:HIS204 3.8 26.6 1.0
NE2 B:HIS204 4.0 30.2 1.0
C B:HIS204 4.1 26.8 1.0
ND1 B:HIS161 4.1 19.6 1.0
C B:CYS196 4.2 27.0 1.0
CD2 B:HIS204 4.2 23.7 1.0
N B:GLU198 4.2 25.6 1.0
O B:CYS196 4.2 24.8 1.0
CA B:CYS200 4.3 27.9 1.0
CA B:ILE199 4.3 28.9 1.0
C B:ILE199 4.3 27.9 1.0
N B:ILE199 4.4 30.2 1.0
SD B:MET207 4.4 29.0 1.0
CA B:CYS196 4.4 27.1 1.0
N B:SER197 4.6 25.4 1.0
CA B:GLU198 4.6 26.9 1.0
CG B:MET207 4.7 26.4 1.0
N B:HIS204 4.7 30.4 1.0
CA B:HIS161 4.8 25.5 1.0
CG B:HIS161 5.0 24.5 1.0
CE1 B:HIS161 5.0 24.8 1.0
CB B:HIS161 5.0 25.2 1.0

Copper binding site 4 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 in the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:37.5
occ:1.00
ND1 N:HIS240 2.0 34.6 1.0
NE2 N:HIS291 2.0 40.0 1.0
N N:CYN520 2.4 42.3 1.0
NE2 N:HIS290 2.6 46.6 1.0
CE1 N:HIS291 2.9 28.6 1.0
CE1 N:HIS240 3.0 28.8 1.0
C N:CYN520 3.0 43.2 1.0
CG N:HIS240 3.0 37.2 1.0
CD2 N:HIS291 3.1 35.3 1.0
CB N:HIS240 3.3 34.7 1.0
CE1 N:HIS290 3.5 41.3 1.0
CD2 N:HIS290 3.7 41.0 1.0
CA N:HIS240 3.8 34.5 1.0
ND1 N:HIS291 4.0 35.1 1.0
NE2 N:HIS240 4.1 32.7 1.0
CD2 N:HIS240 4.1 32.4 1.0
CG N:HIS291 4.1 38.2 1.0
CG2 N:VAL243 4.4 32.4 1.0
N N:HIS240 4.6 30.7 1.0
ND1 N:HIS290 4.7 41.4 1.0
CG1 N:VAL243 4.8 37.1 1.0
CG N:HIS290 4.8 41.6 1.0
O N:HOH4406 4.8 40.0 1.0
C N:HIS240 4.9 34.3 1.0
CG2 N:VAL287 4.9 29.4 1.0
NA N:HEA516 4.9 40.0 1.0
O N:HIS240 4.9 33.8 1.0
C1A N:HEA516 5.0 34.0 1.0
ND N:HEA516 5.0 37.1 1.0

Copper binding site 5 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 in the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:37.1
occ:1.00
CU1 O:CUA228 0.0 37.1 1.0
ND1 O:HIS161 2.0 29.0 1.0
SG O:CYS196 2.3 35.6 1.0
SG O:CYS200 2.4 36.2 1.0
SD O:MET207 2.4 37.9 1.0
CU2 O:CUA228 2.6 36.7 1.0
CE1 O:HIS161 2.8 34.0 1.0
CE O:MET207 3.0 23.3 1.0
CG O:HIS161 3.1 31.9 1.0
CB O:CYS200 3.3 36.8 1.0
CB O:CYS196 3.4 37.1 1.0
CG O:MET207 3.5 35.0 1.0
CB O:HIS161 3.6 31.6 1.0
NE2 O:HIS161 4.0 33.2 1.0
O O:GLU198 4.0 35.8 1.0
CD2 O:HIS161 4.2 34.0 1.0
CA O:HIS161 4.3 34.5 1.0
CD1 O:TRP104 4.3 35.7 1.0
ND1 O:HIS204 4.6 37.3 1.0
O O:HIS102 4.7 31.6 1.0
CA O:CYS200 4.7 36.2 1.0
O O:LEU160 4.7 31.0 1.0
CA O:HIS204 4.8 37.5 1.0
CA O:CYS196 4.8 37.7 1.0
CB O:MET207 4.9 34.8 1.0

Copper binding site 6 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 in the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:36.7
occ:1.00
CU2 O:CUA228 0.0 36.7 1.0
ND1 O:HIS204 2.0 37.3 1.0
O O:GLU198 2.2 35.8 1.0
SG O:CYS196 2.3 35.6 1.0
SG O:CYS200 2.3 36.2 1.0
CU1 O:CUA228 2.6 37.1 1.0
CE1 O:HIS204 2.9 37.4 1.0
CG O:HIS204 3.1 36.0 1.0
CB O:CYS196 3.3 37.1 1.0
CB O:CYS200 3.4 36.8 1.0
C O:GLU198 3.4 35.9 1.0
CB O:HIS204 3.5 35.2 1.0
CA O:HIS204 3.5 37.5 1.0
N O:CYS200 3.7 37.6 1.0
O O:HIS204 3.9 38.5 1.0
NE2 O:HIS204 4.1 37.0 1.0
ND1 O:HIS161 4.1 29.0 1.0
CA O:CYS200 4.1 36.2 1.0
C O:HIS204 4.2 36.6 1.0
CD2 O:HIS204 4.2 32.1 1.0
O O:CYS196 4.2 34.1 1.0
N O:GLU198 4.2 36.2 1.0
C O:CYS196 4.2 37.9 1.0
N O:ILE199 4.3 34.9 1.0
CA O:ILE199 4.3 35.1 1.0
C O:ILE199 4.3 37.0 1.0
CA O:CYS196 4.4 37.7 1.0
CA O:GLU198 4.4 34.9 1.0
SD O:MET207 4.4 37.9 1.0
N O:HIS204 4.7 37.8 1.0
N O:SER197 4.7 38.8 1.0
CG O:MET207 4.8 35.0 1.0
CA O:HIS161 4.9 34.5 1.0
CE1 O:HIS161 4.9 34.0 1.0
CB O:HIS161 5.0 31.6 1.0

Reference:

K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidase Structures Enable O2 Reduction with Minimization of Reactive Oxygens and Provide A Proton-Pumping Gate Proc.Natl.Acad.Sci.Usa V. 107 7740 2010.
ISSN: ISSN 0027-8424
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107
Page generated: Sun Dec 13 11:08:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy