Atomistry » Copper » PDB 7s1d-7xma » 7vvr
Atomistry »
  Copper »
    PDB 7s1d-7xma »
      7vvr »

Copper in PDB 7vvr: Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K

Enzymatic activity of Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K

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

Protein crystallography data

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

Resolution Low / High (Å) 39.95 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.307, 204.706, 177.379, 90, 90, 90
R / Rfree (%) 15.2 / 17.6

Other elements in 7vvr:

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

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

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 7vvr

Go back to Copper Binding Sites List in 7vvr
Copper binding site 1 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence 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 Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:21.7
occ:1.00
N A:CYN606 2.0 22.0 1.0
NE2 A:HIS291 2.0 20.9 1.0
ND1 A:HIS240 2.0 19.9 1.0
NE2 A:HIS290 2.1 22.5 1.0
CE1 A:HIS291 2.9 20.2 1.0
CE1 A:HIS240 3.0 20.7 1.0
CD2 A:HIS291 3.0 21.1 1.0
CE1 A:HIS290 3.0 20.2 1.0
CG A:HIS240 3.1 19.6 1.0
C A:CYN606 3.2 21.7 1.0
CD2 A:HIS290 3.2 24.0 1.0
CB A:HIS240 3.5 20.4 1.0
CA A:HIS240 3.9 21.2 1.0
ND1 A:HIS291 4.0 19.5 1.0
CG A:HIS291 4.1 19.7 1.0
NE2 A:HIS240 4.1 19.4 1.0
CD2 A:HIS240 4.2 19.9 1.0
ND1 A:HIS290 4.2 22.2 1.0
CG A:HIS290 4.3 21.6 1.0
CG2 A:VAL243 4.6 21.2 1.0
NA A:HEA602 4.6 23.0 1.0
C1A A:HEA602 4.7 22.3 1.0
N A:HIS240 4.8 20.8 1.0
C4A A:HEA602 4.9 20.7 1.0
FE A:HEA602 5.0 23.1 1.0
C2A A:HEA602 5.0 22.1 1.0
CG1 A:VAL243 5.0 22.1 1.0

Copper binding site 2 out of 6 in 7vvr

Go back to Copper Binding Sites List in 7vvr
Copper binding site 2 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence 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 Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:24.0
occ:1.00
CU1 B:CUA302 0.0 24.0 1.0
ND1 B:HIS161 2.1 25.6 1.0
SG B:CYS196 2.3 25.3 1.0
SG B:CYS200 2.4 23.6 1.0
SD B:MET207 2.4 25.6 1.0
CU2 B:CUA302 2.5 23.4 1.0
CE1 B:HIS161 3.0 25.6 1.0
CG B:HIS161 3.2 22.1 1.0
CE B:MET207 3.2 24.0 1.0
CB B:CYS200 3.2 24.1 1.0
CB B:CYS196 3.4 24.7 1.0
CG B:MET207 3.4 23.4 1.0
CB B:HIS161 3.6 21.5 1.0
NE2 B:HIS161 4.2 23.0 1.0
CA B:HIS161 4.2 21.5 1.0
O B:GLU198 4.3 26.1 1.0
CD2 B:HIS161 4.3 22.2 1.0
ND1 B:HIS204 4.4 22.4 1.0
CD1 B:TRP104 4.5 24.9 1.0
CA B:CYS200 4.7 22.5 1.0
O B:HIS102 4.7 26.1 1.0
CA B:HIS204 4.7 23.7 1.0
O B:LEU160 4.8 23.1 1.0
CA B:CYS196 4.8 23.6 1.0
CB B:MET207 4.8 25.5 1.0

Copper binding site 3 out of 6 in 7vvr

Go back to Copper Binding Sites List in 7vvr
Copper binding site 3 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence 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 Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:23.4
occ:1.00
CU2 B:CUA302 0.0 23.4 1.0
ND1 B:HIS204 2.0 22.4 1.0
SG B:CYS200 2.2 23.6 1.0
SG B:CYS196 2.3 25.3 1.0
CU1 B:CUA302 2.5 24.0 1.0
O B:GLU198 2.7 26.1 1.0
CE1 B:HIS204 2.9 24.2 1.0
CG B:HIS204 3.1 24.2 1.0
CB B:CYS196 3.3 24.7 1.0
CB B:CYS200 3.3 24.1 1.0
CB B:HIS204 3.5 23.3 1.0
CA B:HIS204 3.5 23.7 1.0
C B:GLU198 3.7 23.1 1.0
N B:CYS200 3.7 23.8 1.0
O B:HIS204 3.8 25.8 1.0
NE2 B:HIS204 4.0 23.9 1.0
CA B:CYS200 4.1 22.5 1.0
CD2 B:HIS204 4.1 22.9 1.0
ND1 B:HIS161 4.2 25.6 1.0
C B:HIS204 4.2 24.7 1.0
C B:CYS196 4.2 23.2 1.0
N B:GLU198 4.2 23.0 1.0
O B:CYS196 4.2 24.2 1.0
CA B:ILE199 4.2 24.1 1.0
C B:ILE199 4.3 23.6 1.0
SD B:MET207 4.3 25.6 1.0
CA B:CYS196 4.4 23.6 1.0
N B:ILE199 4.4 22.2 1.0
CG B:MET207 4.5 23.4 1.0
CA B:GLU198 4.6 24.9 1.0
N B:SER197 4.6 21.9 1.0
N B:HIS204 4.7 25.3 1.0
CA B:HIS161 4.9 21.5 1.0
CB B:HIS161 5.0 21.5 1.0
CG B:HIS161 5.0 22.1 1.0

Copper binding site 4 out of 6 in 7vvr

Go back to Copper Binding Sites List in 7vvr
Copper binding site 4 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence 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 Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:23.5
occ:1.00
ND1 N:HIS240 2.0 20.1 1.0
N N:CYN606 2.0 26.4 1.0
NE2 N:HIS291 2.0 24.3 1.0
NE2 N:HIS290 2.1 25.8 1.0
CE1 N:HIS240 2.9 22.8 1.0
CE1 N:HIS291 2.9 21.5 1.0
CD2 N:HIS291 3.0 26.3 1.0
CG N:HIS240 3.1 19.6 1.0
CE1 N:HIS290 3.1 25.3 1.0
C N:CYN606 3.1 25.5 1.0
CD2 N:HIS290 3.1 23.4 1.0
CB N:HIS240 3.4 21.6 1.0
CA N:HIS240 3.9 21.1 1.0
ND1 N:HIS291 4.0 20.9 1.0
NE2 N:HIS240 4.1 21.5 1.0
CG N:HIS291 4.1 22.8 1.0
CD2 N:HIS240 4.2 20.6 1.0
ND1 N:HIS290 4.2 23.4 1.0
CG N:HIS290 4.3 23.3 1.0
CG2 N:VAL243 4.6 23.7 1.0
NA N:HEA602 4.6 25.8 1.0
C1A N:HEA602 4.8 25.7 1.0
N N:HIS240 4.8 22.0 1.0
C4A N:HEA602 4.8 22.1 1.0
FE N:HEA602 5.0 24.9 1.0
CG1 N:VAL243 5.0 24.7 1.0

Copper binding site 5 out of 6 in 7vvr

Go back to Copper Binding Sites List in 7vvr
Copper binding site 5 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence 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 Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:28.4
occ:1.00
CU1 O:CUA302 0.0 28.4 1.0
ND1 O:HIS161 2.1 27.9 1.0
SD O:MET207 2.3 30.6 1.0
SG O:CYS196 2.3 28.8 1.0
SG O:CYS200 2.4 29.4 1.0
CU2 O:CUA302 2.5 27.9 1.0
CE1 O:HIS161 2.9 27.4 1.0
CE O:MET207 3.1 29.8 1.0
CG O:HIS161 3.2 25.6 1.0
CB O:CYS200 3.3 26.3 1.0
CB O:CYS196 3.4 30.9 1.0
CG O:MET207 3.4 26.9 1.0
CB O:HIS161 3.6 26.2 1.0
NE2 O:HIS161 4.1 27.6 1.0
CA O:HIS161 4.2 27.1 1.0
O O:GLU198 4.2 27.9 1.0
CD2 O:HIS161 4.2 28.1 1.0
CD1 O:TRP104 4.4 32.3 1.0
ND1 O:HIS204 4.4 28.9 1.0
O O:HIS102 4.7 31.1 1.0
CA O:CYS200 4.7 28.1 1.0
O O:LEU160 4.7 27.4 1.0
CA O:HIS204 4.7 30.2 1.0
CA O:CYS196 4.8 25.8 1.0
CB O:MET207 4.8 29.7 1.0
N O:CYS200 5.0 27.4 1.0

Copper binding site 6 out of 6 in 7vvr

Go back to Copper Binding Sites List in 7vvr
Copper binding site 6 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence 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 Mixed Valence State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:27.9
occ:1.00
CU2 O:CUA302 0.0 27.9 1.0
ND1 O:HIS204 2.0 28.9 1.0
SG O:CYS200 2.3 29.4 1.0
SG O:CYS196 2.3 28.8 1.0
CU1 O:CUA302 2.5 28.4 1.0
O O:GLU198 2.7 27.9 1.0
CE1 O:HIS204 2.9 26.1 1.0
CG O:HIS204 3.1 28.4 1.0
CB O:CYS196 3.2 30.9 1.0
CB O:CYS200 3.4 26.3 1.0
CA O:HIS204 3.5 30.2 1.0
CB O:HIS204 3.6 27.0 1.0
N O:CYS200 3.7 27.4 1.0
C O:GLU198 3.7 26.4 1.0
O O:HIS204 3.8 29.9 1.0
NE2 O:HIS204 4.0 26.7 1.0
ND1 O:HIS161 4.1 27.9 1.0
CA O:CYS200 4.2 28.1 1.0
C O:HIS204 4.2 29.2 1.0
CD2 O:HIS204 4.2 26.3 1.0
C O:CYS196 4.2 28.6 1.0
N O:GLU198 4.2 27.2 1.0
O O:CYS196 4.2 28.4 1.0
CA O:ILE199 4.3 27.5 1.0
C O:ILE199 4.3 27.2 1.0
SD O:MET207 4.3 30.6 1.0
CA O:CYS196 4.3 25.8 1.0
N O:ILE199 4.4 25.7 1.0
CG O:MET207 4.5 26.9 1.0
N O:SER197 4.6 27.5 1.0
CA O:GLU198 4.6 29.0 1.0
N O:HIS204 4.7 29.5 1.0
CA O:HIS161 4.9 27.1 1.0
CB O:HIS161 5.0 26.2 1.0

Reference:

A.Shimada, T.Tsukihara. Bovine Cytochrome C Oxidese in Cn-Bound Mixed Valence State at 50 K To Be Published.
Page generated: Tue Apr 4 23:29:02 2023

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