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Copper in PDB 7w3e: Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K

Enzymatic activity of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K

All present enzymatic activity of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K:
1.9.3.1; 7.1.1.9;

Protein crystallography data

The structure of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K, PDB code: 7w3e was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.76 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.666, 203.752, 177.683, 90, 90, 90
R / Rfree (%) 16.2 / 18.2

Other elements in 7w3e:

The structure of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K also contains other interesting chemical elements:

Sodium (Na) 4 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 6 atoms
Zinc (Zn) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K (pdb code 7w3e). 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 Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K, PDB code: 7w3e:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7w3e

Go back to Copper Binding Sites List in 7w3e
Copper binding site 1 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:23.5
occ:1.00
 ND1 A:HIS240 1.9 20.9 1.0
NE2 A:HIS291 2.0 20.2 1.0
N A:CYN606 2.0 24.9 0.5
N A:CYN606 2.2 18.8 0.5
NE2 A:HIS290 2.2 24.2 0.5
CE1 A:HIS240 2.9 22.7 1.0
CE1 A:HIS291 2.9 21.5 1.0
CG A:HIS240 3.0 19.1 1.0
CD2 A:HIS291 3.0 21.1 1.0
CE1 A:HIS290 3.0 29.1 0.5
NE2 A:HIS290 3.1 18.3 0.5
C A:CYN606 3.1 25.2 0.5
C A:CYN606 3.3 17.8 0.5
CB A:HIS240 3.3 22.4 1.0
CD2 A:HIS290 3.4 22.4 0.5
CA A:HIS240 3.8 21.0 1.0
CE1 A:HIS290 3.9 19.2 0.5
CD2 A:HIS290 4.0 15.4 0.5
NE2 A:HIS240 4.0 21.0 1.0
ND1 A:HIS291 4.0 21.9 1.0
CD2 A:HIS240 4.1 20.3 1.0
CG A:HIS291 4.1 21.1 1.0
ND1 A:HIS290 4.2 26.1 0.5
CG A:HIS290 4.4 20.2 0.5
CG2 A:VAL243 4.5 23.1 1.0
N A:HIS240 4.6 21.2 1.0
NA A:HEA602 4.7 21.1 0.5
C1A A:HEA602 4.8 21.4 0.5
ND A:HEA602 4.8 26.4 0.5
ND1 A:HIS290 4.8 18.3 0.5
C A:HIS240 4.9 19.7 1.0
O A:HOH822 4.9 22.9 0.7
C4D A:HEA602 4.9 19.3 0.5
CG A:HIS290 4.9 20.0 0.5
CG2 A:VAL287 4.9 22.1 1.0
CG1 A:VAL243 5.0 22.1 1.0
O A:HIS240 5.0 20.0 1.0
CZ3 A:TRP236 5.0 24.4 1.0

Copper binding site 2 out of 6 in 7w3e

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Copper binding site 2 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:24.4
occ:1.00
 CU1 B:CUA302 0.0 24.4 1.0
ND1 B:HIS161 2.1 24.7 1.0
SD B:MET207 2.4 25.0 1.0
SG B:CYS196 2.4 24.0 1.0
SG B:CYS200 2.4 24.2 1.0
CU2 B:CUA302 2.5 24.0 1.0
CE1 B:HIS161 2.9 24.0 1.0
CG B:HIS161 3.2 22.8 1.0
CE B:MET207 3.2 27.2 1.0
CB B:CYS200 3.3 23.4 1.0
CB B:CYS196 3.4 23.8 1.0
CG B:MET207 3.6 23.0 1.0
CB B:HIS161 3.6 22.6 1.0
NE2 B:HIS161 4.1 23.0 1.0
CA B:HIS161 4.2 22.0 1.0
CD2 B:HIS161 4.3 23.4 1.0
O B:GLU198 4.3 23.7 1.0
ND1 B:HIS204 4.4 23.7 1.0
CD1 B:TRP104 4.5 26.8 1.0
O B:HIS102 4.7 25.8 1.0
CA B:CYS200 4.7 23.3 1.0
CA B:HIS204 4.7 23.5 1.0
O B:LEU160 4.8 23.5 1.0
CA B:CYS196 4.8 22.9 1.0
CB B:MET207 4.9 22.9 1.0

Copper binding site 3 out of 6 in 7w3e

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Copper binding site 3 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:24.0
occ:1.00
 CU2 B:CUA302 0.0 24.0 1.0
ND1 B:HIS204 2.0 23.7 1.0
SG B:CYS196 2.3 24.0 1.0
SG B:CYS200 2.3 24.2 1.0
CU1 B:CUA302 2.5 24.4 1.0
O B:GLU198 2.7 23.7 1.0
CE1 B:HIS204 2.9 23.2 1.0
CG B:HIS204 3.1 23.1 1.0
CB B:CYS196 3.2 23.8 1.0
CB B:CYS200 3.4 23.4 1.0
CB B:HIS204 3.6 21.7 1.0
CA B:HIS204 3.6 23.5 1.0
N B:CYS200 3.7 23.5 1.0
C B:GLU198 3.8 23.6 1.0
O B:HIS204 3.8 25.4 1.0
NE2 B:HIS204 4.1 23.8 1.0
ND1 B:HIS161 4.1 24.7 1.0
C B:CYS196 4.1 21.7 1.0
C B:HIS204 4.2 24.5 1.0
CD2 B:HIS204 4.2 23.9 1.0
N B:GLU198 4.2 22.5 1.0
CA B:CYS200 4.2 23.3 1.0
O B:CYS196 4.2 23.8 1.0
SD B:MET207 4.3 25.0 1.0
CA B:ILE199 4.3 22.7 1.0
CA B:CYS196 4.3 22.9 1.0
C B:ILE199 4.3 23.4 1.0
N B:ILE199 4.5 23.7 1.0
N B:SER197 4.6 22.1 1.0
CG B:MET207 4.6 23.0 1.0
CA B:GLU198 4.7 22.4 1.0
N B:HIS204 4.7 25.3 1.0
CA B:HIS161 4.8 22.0 1.0
CB B:HIS161 5.0 22.6 1.0
CG B:HIS161 5.0 22.8 1.0

Copper binding site 4 out of 6 in 7w3e

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Copper binding site 4 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:25.2
occ:1.00
 NE2 N:HIS291 1.9 21.8 1.0
ND1 N:HIS240 1.9 24.3 1.0
N N:CYN606 2.0 26.4 0.6
N N:CYN606 2.1 24.9 0.4
NE2 N:HIS290 2.3 28.4 0.6
CE1 N:HIS291 2.9 23.7 1.0
CE1 N:HIS240 3.0 24.7 1.0
CD2 N:HIS291 3.0 24.0 1.0
CG N:HIS240 3.0 22.6 1.0
CE1 N:HIS290 3.1 28.7 0.6
C N:CYN606 3.2 28.9 0.6
C N:CYN606 3.2 20.2 0.4
NE2 N:HIS290 3.2 18.7 0.4
CB N:HIS240 3.3 22.3 1.0
CD2 N:HIS290 3.4 23.3 0.6
CA N:HIS240 3.8 22.9 1.0
CE1 N:HIS290 3.9 21.9 0.4
ND1 N:HIS291 4.0 26.0 1.0
CD2 N:HIS290 4.0 15.9 0.4
NE2 N:HIS240 4.1 22.4 1.0
CG N:HIS291 4.1 23.9 1.0
CD2 N:HIS240 4.1 23.3 1.0
ND1 N:HIS290 4.3 27.7 0.6
CG N:HIS290 4.4 19.1 0.6
CG2 N:VAL243 4.5 24.8 1.0
N N:HIS240 4.6 22.1 1.0
NA N:HEA602 4.7 23.9 0.6
C1A N:HEA602 4.8 21.4 0.6
ND N:HEA602 4.9 23.8 0.4
ND1 N:HIS290 4.9 19.9 0.4
C N:HIS240 4.9 22.6 1.0
C4D N:HEA602 4.9 20.7 0.4
O N:HOH787 5.0 25.9 0.7
CG N:HIS290 5.0 26.2 0.4
O N:HIS240 5.0 22.4 1.0
CZ3 N:TRP236 5.0 25.9 1.0
CG2 N:VAL287 5.0 24.2 1.0

Copper binding site 5 out of 6 in 7w3e

Go back to Copper Binding Sites List in 7w3e
Copper binding site 5 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu303

b:28.1
occ:1.00
 CU1 O:CUA303 0.0 28.1 1.0
ND1 O:HIS161 2.1 28.9 1.0
SG O:CYS196 2.3 28.8 1.0
SG O:CYS200 2.4 29.4 1.0
SD O:MET207 2.4 30.5 1.0
CU2 O:CUA303 2.5 27.6 1.0
CE1 O:HIS161 2.9 26.9 1.0
CE O:MET207 3.2 29.9 1.0
CG O:HIS161 3.2 26.6 1.0
CB O:CYS200 3.3 26.7 1.0
CB O:CYS196 3.4 27.9 1.0
CG O:MET207 3.5 28.6 1.0
CB O:HIS161 3.6 27.8 1.0
NE2 O:HIS161 4.1 27.5 1.0
CA O:HIS161 4.2 27.1 1.0
CD2 O:HIS161 4.2 28.6 1.0
O O:GLU198 4.3 27.6 1.0
CD1 O:TRP104 4.4 32.8 1.0
ND1 O:HIS204 4.5 28.6 1.0
O O:HIS102 4.6 29.8 1.0
CA O:CYS200 4.7 27.4 1.0
CA O:HIS204 4.7 29.6 1.0
O O:LEU160 4.8 28.5 1.0
CA O:CYS196 4.8 28.5 1.0
CB O:MET207 4.9 29.5 1.0

Copper binding site 6 out of 6 in 7w3e

Go back to Copper Binding Sites List in 7w3e
Copper binding site 6 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu303

b:27.6
occ:1.00
 CU2 O:CUA303 0.0 27.6 1.0
ND1 O:HIS204 2.0 28.6 1.0
SG O:CYS200 2.3 29.4 1.0
SG O:CYS196 2.3 28.8 1.0
CU1 O:CUA303 2.5 28.1 1.0
O O:GLU198 2.7 27.6 1.0
CE1 O:HIS204 2.9 27.3 1.0
CG O:HIS204 3.1 26.7 1.0
CB O:CYS196 3.2 27.9 1.0
CB O:CYS200 3.4 26.7 1.0
CA O:HIS204 3.5 29.6 1.0
CB O:HIS204 3.6 28.0 1.0
N O:CYS200 3.7 29.1 1.0
C O:GLU198 3.7 27.7 1.0
O O:HIS204 3.9 29.4 1.0
NE2 O:HIS204 4.1 27.8 1.0
C O:HIS204 4.1 27.7 1.0
CA O:CYS200 4.2 27.4 1.0
ND1 O:HIS161 4.2 28.9 1.0
C O:CYS196 4.2 28.5 1.0
CD2 O:HIS204 4.2 27.7 1.0
N O:GLU198 4.2 26.2 1.0
O O:CYS196 4.2 28.9 1.0
CA O:CYS196 4.3 28.5 1.0
C O:ILE199 4.3 28.2 1.0
CA O:ILE199 4.3 27.7 1.0
SD O:MET207 4.3 30.5 1.0
N O:ILE199 4.5 27.1 1.0
N O:SER197 4.6 26.9 1.0
CG O:MET207 4.6 28.6 1.0
CA O:GLU198 4.6 26.4 1.0
N O:HIS204 4.7 28.3 1.0
CA O:HIS161 4.9 27.1 1.0
CB O:HIS161 5.0 27.8 1.0

Reference:

A.Shimada, J.Baba, K.Shinzawa-Itoh, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K. To Be Published.
Page generated: Wed Jul 31 09:19:02 2024

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