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Copper in PDB 3ag3: Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K

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

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 3ag3 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 (°) 182.289, 208.358, 177.916, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.3

Other elements in 3ag3:

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-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 Nitric Oxide-Bound Fully Reduced State at 100 K (pdb code 3ag3). 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 Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 3ag3:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3ag3

Go back to Copper Binding Sites List in 3ag3
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:24.6
occ:1.00
NE2 A:HIS291 2.0 22.6 1.0
ND1 A:HIS240 2.0 22.7 1.0
NE2 A:HIS290 2.0 24.6 1.0
O A:NO520 2.5 24.9 1.0
CD2 A:HIS291 2.9 21.9 1.0
CE1 A:HIS290 2.9 21.8 1.0
CE1 A:HIS291 3.0 24.3 1.0
CG A:HIS240 3.0 21.9 1.0
CE1 A:HIS240 3.0 19.5 1.0
CD2 A:HIS290 3.0 23.8 1.0
N A:NO520 3.3 25.8 1.0
CB A:HIS240 3.3 21.0 1.0
CA A:HIS240 3.8 19.8 1.0
CG A:HIS291 4.0 23.7 1.0
ND1 A:HIS291 4.1 20.9 1.0
ND1 A:HIS290 4.1 23.1 1.0
CD2 A:HIS240 4.1 21.3 1.0
CG A:HIS290 4.1 21.1 1.0
NE2 A:HIS240 4.1 21.0 1.0
NA A:HEA516 4.6 20.0 1.0
C1A A:HEA516 4.6 20.3 1.0
CG2 A:VAL243 4.8 21.4 1.0
N A:HIS240 4.8 19.7 1.0
C4A A:HEA516 4.8 20.8 1.0
FE A:HEA516 4.9 23.1 1.0
C2A A:HEA516 4.9 22.0 1.0
CG2 A:VAL287 4.9 22.2 1.0
CA A:TRP288 5.0 22.6 1.0

Copper binding site 2 out of 6 in 3ag3

Go back to Copper Binding Sites List in 3ag3
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:23.9
occ:1.00
CU1 B:CUA228 0.0 23.9 1.0
ND1 B:HIS161 2.1 22.9 1.0
SG B:CYS196 2.3 23.1 1.0
SD B:MET207 2.4 23.2 1.0
SG B:CYS200 2.4 21.9 1.0
CU2 B:CUA228 2.5 23.8 1.0
CE1 B:HIS161 3.0 20.7 1.0
CE B:MET207 3.1 25.4 1.0
CG B:HIS161 3.2 15.3 1.0
CB B:CYS200 3.3 22.1 1.0
CG B:MET207 3.5 22.9 1.0
CB B:CYS196 3.5 21.5 1.0
CB B:HIS161 3.6 18.6 1.0
O B:GLU198 4.2 24.2 1.0
NE2 B:HIS161 4.2 21.0 1.0
CA B:HIS161 4.3 19.0 1.0
CD2 B:HIS161 4.3 21.7 1.0
CD1 B:TRP104 4.5 24.9 1.0
ND1 B:HIS204 4.5 24.7 1.0
O B:HIS102 4.7 22.6 1.0
CA B:CYS200 4.7 21.4 1.0
CA B:HIS204 4.8 23.9 1.0
O B:LEU160 4.8 22.7 1.0
CA B:CYS196 4.9 22.8 1.0
CB B:MET207 4.9 24.1 1.0
CZ2 B:TRP106 5.0 23.5 1.0

Copper binding site 3 out of 6 in 3ag3

Go back to Copper Binding Sites List in 3ag3
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-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 Nitric Oxide-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 2.1 24.7 1.0
SG B:CYS200 2.3 21.9 1.0
SG B:CYS196 2.3 23.1 1.0
CU1 B:CUA228 2.5 23.9 1.0
O B:GLU198 2.5 24.2 1.0
CE1 B:HIS204 3.0 22.8 1.0
CG B:HIS204 3.1 24.9 1.0
CB B:CYS196 3.3 21.5 1.0
CB B:CYS200 3.4 22.1 1.0
CB B:HIS204 3.5 22.2 1.0
CA B:HIS204 3.6 23.9 1.0
C B:GLU198 3.7 22.8 1.0
N B:CYS200 3.7 21.4 1.0
O B:HIS204 3.9 23.9 1.0
NE2 B:HIS204 4.1 22.7 1.0
C B:HIS204 4.2 21.6 1.0
ND1 B:HIS161 4.2 22.9 1.0
CA B:CYS200 4.2 21.4 1.0
N B:GLU198 4.2 21.7 1.0
CD2 B:HIS204 4.2 24.8 1.0
C B:CYS196 4.2 22.5 1.0
O B:CYS196 4.2 22.8 1.0
CA B:ILE199 4.3 22.3 1.0
C B:ILE199 4.3 22.0 1.0
SD B:MET207 4.4 23.2 1.0
N B:ILE199 4.4 22.3 1.0
CA B:CYS196 4.5 22.8 1.0
N B:SER197 4.6 22.7 1.0
CA B:GLU198 4.6 22.1 1.0
CG B:MET207 4.7 22.9 1.0
N B:HIS204 4.8 24.2 1.0
CA B:HIS161 4.9 19.0 1.0
C B:CYS200 5.0 20.1 1.0

Copper binding site 4 out of 6 in 3ag3

Go back to Copper Binding Sites List in 3ag3
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:26.7
occ:1.00
ND1 N:HIS240 2.0 27.2 1.0
NE2 N:HIS291 2.0 27.9 1.0
NE2 N:HIS290 2.0 26.0 1.0
O N:NO520 2.5 26.3 1.0
CD2 N:HIS291 2.9 28.1 1.0
CG N:HIS240 3.0 24.3 1.0
CE1 N:HIS240 3.0 25.0 1.0
CD2 N:HIS290 3.0 25.8 1.0
CE1 N:HIS291 3.0 27.2 1.0
CE1 N:HIS290 3.0 26.9 1.0
N N:NO520 3.3 32.0 1.0
CB N:HIS240 3.3 22.4 1.0
CA N:HIS240 3.8 23.2 1.0
CG N:HIS291 4.1 28.0 1.0
ND1 N:HIS291 4.1 25.8 1.0
NE2 N:HIS240 4.1 25.8 1.0
CD2 N:HIS240 4.1 23.5 1.0
ND1 N:HIS290 4.1 24.0 1.0
CG N:HIS290 4.1 24.9 1.0
NA N:HEA516 4.6 25.8 1.0
C1A N:HEA516 4.6 27.4 1.0
CG2 N:VAL243 4.7 24.3 1.0
N N:HIS240 4.8 23.7 1.0
C4A N:HEA516 4.8 24.2 1.0
FE N:HEA516 4.9 26.2 1.0
CG2 N:VAL287 5.0 27.8 1.0
C2A N:HEA516 5.0 24.9 1.0

Copper binding site 5 out of 6 in 3ag3

Go back to Copper Binding Sites List in 3ag3
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:28.0
occ:1.00
CU1 O:CUA228 0.0 28.0 1.0
ND1 O:HIS161 2.1 27.4 1.0
SG O:CYS196 2.3 29.0 1.0
SG O:CYS200 2.4 25.2 1.0
SD O:MET207 2.4 25.0 1.0
CU2 O:CUA228 2.5 27.8 1.0
CE1 O:HIS161 3.0 27.3 1.0
CE O:MET207 3.1 28.0 1.0
CG O:HIS161 3.2 28.5 1.0
CB O:CYS200 3.3 26.7 1.0
CG O:MET207 3.4 24.5 1.0
CB O:CYS196 3.6 26.2 1.0
CB O:HIS161 3.6 25.5 1.0
O O:GLU198 4.1 27.3 1.0
CA O:HIS161 4.2 24.6 1.0
NE2 O:HIS161 4.2 28.4 1.0
CD2 O:HIS161 4.3 24.3 1.0
ND1 O:HIS204 4.5 28.3 1.0
CD1 O:TRP104 4.5 29.7 1.0
CA O:CYS200 4.7 26.6 1.0
CA O:HIS204 4.7 26.9 1.0
O O:HIS102 4.7 26.6 1.0
O O:LEU160 4.8 25.9 1.0
CB O:MET207 4.9 27.3 1.0
N O:CYS200 4.9 27.5 1.0
CA O:CYS196 5.0 27.5 1.0

Copper binding site 6 out of 6 in 3ag3

Go back to Copper Binding Sites List in 3ag3
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:27.8
occ:1.00
CU2 O:CUA228 0.0 27.8 1.0
ND1 O:HIS204 2.0 28.3 1.0
SG O:CYS200 2.2 25.2 1.0
SG O:CYS196 2.3 29.0 1.0
O O:GLU198 2.4 27.3 1.0
CU1 O:CUA228 2.5 28.0 1.0
CE1 O:HIS204 2.9 28.6 1.0
CG O:HIS204 3.1 28.9 1.0
CB O:CYS196 3.4 26.2 1.0
CB O:CYS200 3.4 26.7 1.0
CB O:HIS204 3.5 24.2 1.0
CA O:HIS204 3.5 26.9 1.0
N O:CYS200 3.6 27.5 1.0
C O:GLU198 3.6 27.7 1.0
O O:HIS204 3.9 29.2 1.0
NE2 O:HIS204 4.1 31.1 1.0
N O:GLU198 4.2 25.2 1.0
CA O:CYS200 4.2 26.6 1.0
CD2 O:HIS204 4.2 24.8 1.0
C O:HIS204 4.2 27.6 1.0
ND1 O:HIS161 4.2 27.4 1.0
C O:ILE199 4.2 28.5 1.0
CA O:ILE199 4.3 24.6 1.0
O O:CYS196 4.3 27.1 1.0
C O:CYS196 4.3 27.9 1.0
SD O:MET207 4.4 25.0 1.0
N O:ILE199 4.4 26.7 1.0
CA O:CYS196 4.5 27.5 1.0
CA O:GLU198 4.6 25.4 1.0
CG O:MET207 4.6 24.5 1.0
N O:SER197 4.6 28.2 1.0
N O:HIS204 4.8 27.4 1.0
CA O:HIS161 4.9 24.6 1.0
CB O:HIS161 5.0 25.5 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 11:08:50 2020

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