Atomistry » Copper » PDB 2idq-2pp7 » 3ag2
Atomistry »
  Copper »
    PDB 2idq-2pp7 »
      3ag2 »

Copper in PDB 3ag2: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K

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

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K, PDB code: 3ag2 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 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.834, 206.933, 178.090, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.3

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 100 K (pdb code 3ag2). 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 Carbon Monoxide-Bound Fully Reduced State at 100 K, PDB code: 3ag2:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3ag2

Go back to Copper Binding Sites List in 3ag2
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-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 Carbon Monoxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:22.4
occ:1.00
NE2 A:HIS291 2.0 27.7 1.0
NE2 A:HIS290 2.0 21.8 1.0
ND1 A:HIS240 2.0 30.1 1.0
C A:CMO520 2.4 25.8 1.0
O A:CMO520 2.7 25.5 1.0
CE1 A:HIS291 2.9 22.8 1.0
CD2 A:HIS291 2.9 21.1 1.0
CE1 A:HIS290 3.0 26.0 1.0
CE1 A:HIS240 3.0 18.0 1.0
CD2 A:HIS290 3.0 19.5 1.0
CG A:HIS240 3.2 24.9 1.0
CB A:HIS240 3.6 21.0 1.0
ND1 A:HIS291 4.0 20.6 1.0
CG A:HIS291 4.0 23.8 1.0
ND1 A:HIS290 4.1 23.2 1.0
CA A:HIS240 4.2 18.3 1.0
NE2 A:HIS240 4.2 26.2 1.0
CG A:HIS290 4.2 24.4 1.0
CD2 A:HIS240 4.3 33.2 1.0
NA A:HEA516 4.3 26.2 1.0
C1A A:HEA516 4.3 19.6 1.0
C4A A:HEA516 4.4 15.9 1.0
C2A A:HEA516 4.5 18.4 1.0
CG2 A:VAL243 4.7 21.5 1.0
C3A A:HEA516 4.7 18.0 1.0
CHA A:HEA516 4.9 20.4 1.0
FE A:HEA516 5.0 22.6 1.0

Copper binding site 2 out of 6 in 3ag2

Go back to Copper Binding Sites List in 3ag2
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-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 Carbon Monoxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:24.7
occ:1.00
CU1 B:CUA228 0.0 24.7 1.0
ND1 B:HIS161 2.0 22.9 1.0
SG B:CYS196 2.3 22.8 1.0
SG B:CYS200 2.4 20.9 1.0
SD B:MET207 2.4 24.7 1.0
CU2 B:CUA228 2.6 23.8 1.0
CE1 B:HIS161 2.9 20.1 1.0
CE B:MET207 3.0 16.4 1.0
CG B:HIS161 3.2 12.2 1.0
CB B:CYS200 3.4 23.0 1.0
CB B:CYS196 3.6 20.4 1.0
CB B:HIS161 3.6 17.2 1.0
CG B:MET207 3.6 26.3 1.0
O B:GLU198 4.1 28.2 1.0
CA B:HIS161 4.1 17.5 1.0
NE2 B:HIS161 4.1 19.8 1.0
CD2 B:HIS161 4.3 22.4 1.0
ND1 B:HIS204 4.5 29.0 1.0
CD1 B:TRP104 4.6 21.5 1.0
O B:LEU160 4.7 22.9 1.0
O B:HIS102 4.8 20.0 1.0
CA B:CYS200 4.8 18.9 1.0
CA B:HIS204 4.8 19.9 1.0
CA B:CYS196 4.9 24.1 1.0
CB B:MET207 5.0 23.4 1.0
N B:SER162 5.0 21.7 1.0
O B:HIS204 5.0 21.6 1.0

Copper binding site 3 out of 6 in 3ag2

Go back to Copper Binding Sites List in 3ag2
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-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 Carbon Monoxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:23.8
occ:1.00
CU2 B:CUA228 0.0 23.8 1.0
ND1 B:HIS204 2.0 29.0 1.0
SG B:CYS200 2.2 20.9 1.0
SG B:CYS196 2.4 22.8 1.0
O B:GLU198 2.4 28.2 1.0
CU1 B:CUA228 2.6 24.7 1.0
CE1 B:HIS204 2.9 24.5 1.0
CG B:HIS204 3.1 24.0 1.0
CB B:CYS196 3.4 20.4 1.0
CB B:HIS204 3.5 20.6 1.0
C B:GLU198 3.6 24.6 1.0
CA B:HIS204 3.6 19.9 1.0
CB B:CYS200 3.6 23.0 1.0
N B:CYS200 3.7 23.1 1.0
O B:HIS204 3.8 21.6 1.0
NE2 B:HIS204 4.1 23.7 1.0
C B:HIS204 4.1 23.1 1.0
CD2 B:HIS204 4.2 23.8 1.0
ND1 B:HIS161 4.2 22.9 1.0
C B:ILE199 4.2 25.3 1.0
N B:GLU198 4.2 23.9 1.0
C B:CYS196 4.2 20.1 1.0
CA B:CYS200 4.2 18.9 1.0
O B:CYS196 4.3 16.3 1.0
CA B:ILE199 4.3 24.4 1.0
N B:ILE199 4.3 24.1 1.0
SD B:MET207 4.4 24.7 1.0
CA B:CYS196 4.5 24.1 1.0
CA B:GLU198 4.6 22.6 1.0
N B:SER197 4.6 22.9 1.0
CG B:MET207 4.8 26.3 1.0
N B:HIS204 4.8 24.0 1.0
CA B:HIS161 4.8 17.5 1.0

Copper binding site 4 out of 6 in 3ag2

Go back to Copper Binding Sites List in 3ag2
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-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 Carbon Monoxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:29.1
occ:1.00
NE2 N:HIS290 1.9 30.0 1.0
NE2 N:HIS291 2.0 30.7 1.0
ND1 N:HIS240 2.0 30.8 1.0
C N:CMO520 2.5 30.9 1.0
O N:CMO520 2.6 30.1 1.0
CE1 N:HIS290 2.8 31.9 1.0
CE1 N:HIS240 2.9 24.5 1.0
CE1 N:HIS291 3.0 25.9 1.0
CD2 N:HIS291 3.0 27.2 1.0
CD2 N:HIS290 3.1 29.0 1.0
CG N:HIS240 3.2 27.7 1.0
CB N:HIS240 3.6 25.8 1.0
ND1 N:HIS290 4.0 29.6 1.0
ND1 N:HIS291 4.0 28.1 1.0
NE2 N:HIS240 4.1 29.0 1.0
CG N:HIS291 4.1 32.4 1.0
CG N:HIS290 4.1 29.4 1.0
CA N:HIS240 4.1 25.1 1.0
CD2 N:HIS240 4.2 30.5 1.0
NA N:HEA516 4.3 31.1 1.0
C1A N:HEA516 4.4 29.0 1.0
C4A N:HEA516 4.4 26.1 1.0
C2A N:HEA516 4.6 28.5 1.0
C3A N:HEA516 4.6 27.1 1.0
CG2 N:VAL243 4.8 24.1 1.0
CHA N:HEA516 4.8 21.4 1.0
FE N:HEA516 5.0 29.0 1.0

Copper binding site 5 out of 6 in 3ag2

Go back to Copper Binding Sites List in 3ag2
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-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 Carbon Monoxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:31.5
occ:1.00
CU1 O:CUA228 0.0 31.5 1.0
ND1 O:HIS161 2.0 30.8 1.0
SG O:CYS196 2.3 30.8 1.0
SD O:MET207 2.4 32.6 1.0
SG O:CYS200 2.4 29.4 1.0
CU2 O:CUA228 2.5 31.7 1.0
CE1 O:HIS161 2.9 28.7 1.0
CG O:HIS161 3.1 22.7 1.0
CE O:MET207 3.2 20.8 1.0
CB O:CYS200 3.3 30.6 1.0
CG O:MET207 3.5 26.5 1.0
CB O:CYS196 3.5 29.1 1.0
CB O:HIS161 3.6 29.6 1.0
O O:GLU198 4.0 31.7 1.0
NE2 O:HIS161 4.0 28.7 1.0
CD2 O:HIS161 4.2 30.4 1.0
CA O:HIS161 4.3 29.8 1.0
CD1 O:TRP104 4.5 31.0 1.0
ND1 O:HIS204 4.5 35.9 1.0
O O:HIS102 4.7 27.4 1.0
CA O:CYS200 4.7 29.9 1.0
CA O:HIS204 4.7 30.0 1.0
O O:LEU160 4.8 30.5 1.0
CA O:CYS196 4.9 30.2 1.0
CB O:MET207 4.9 29.0 1.0
O O:HIS204 5.0 30.5 1.0
N O:CYS200 5.0 30.0 1.0

Copper binding site 6 out of 6 in 3ag2

Go back to Copper Binding Sites List in 3ag2
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-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 Carbon Monoxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:31.7
occ:1.00
CU2 O:CUA228 0.0 31.7 1.0
ND1 O:HIS204 2.0 35.9 1.0
SG O:CYS200 2.3 29.4 1.0
SG O:CYS196 2.3 30.8 1.0
O O:GLU198 2.3 31.7 1.0
CU1 O:CUA228 2.5 31.5 1.0
CE1 O:HIS204 2.9 32.5 1.0
CG O:HIS204 3.1 29.1 1.0
CB O:CYS196 3.3 29.1 1.0
CB O:CYS200 3.4 30.6 1.0
CB O:HIS204 3.5 28.5 1.0
C O:GLU198 3.5 28.4 1.0
CA O:HIS204 3.5 30.0 1.0
N O:CYS200 3.7 30.0 1.0
O O:HIS204 3.8 30.5 1.0
NE2 O:HIS204 4.1 33.6 1.0
ND1 O:HIS161 4.1 30.8 1.0
CD2 O:HIS204 4.2 27.6 1.0
C O:HIS204 4.2 30.1 1.0
N O:GLU198 4.2 29.0 1.0
CA O:CYS200 4.2 29.9 1.0
O O:CYS196 4.2 29.4 1.0
C O:ILE199 4.2 30.3 1.0
CA O:ILE199 4.3 29.3 1.0
C O:CYS196 4.3 30.1 1.0
N O:ILE199 4.3 27.8 1.0
SD O:MET207 4.4 32.6 1.0
CA O:CYS196 4.4 30.2 1.0
CA O:GLU198 4.5 30.0 1.0
CG O:MET207 4.7 26.5 1.0
N O:SER197 4.7 31.5 1.0
N O:HIS204 4.7 30.4 1.0
CA O:HIS161 4.9 29.8 1.0
CB O:HIS161 4.9 29.6 1.0
CG O:HIS161 4.9 22.7 1.0
CE1 O:HIS161 5.0 28.7 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: Thu Sep 3 17:05:15 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy