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Copper in PDB 7y44: Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution

Enzymatic activity of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution

All present enzymatic activity of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution, PDB code: 7y44 was solved by T.Tsukihara, K.Hirata, H.Ago, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.31 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.6, 204.51, 178.29, 90, 90, 90
R / Rfree (%) 18.5 / 22.7

Other elements in 7y44:

The structure of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution (pdb code 7y44). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution, PDB code: 7y44:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7y44

Go back to Copper Binding Sites List in 7y44
Copper binding site 1 out of 6 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:17.1
occ:1.00
 NE2 A:HIS291 2.0 16.4 1.0
NE2 A:HIS290 2.0 15.8 1.0
ND1 A:HIS240 2.0 17.1 1.0
O2 A:PER606 2.1 15.8 1.0
O1 A:PER606 2.7 12.6 1.0
CE1 A:HIS290 2.9 18.9 1.0
CE1 A:HIS291 2.9 17.1 1.0
CD2 A:HIS291 3.0 14.7 1.0
CE1 A:HIS240 3.0 17.2 1.0
CG A:HIS240 3.0 18.3 1.0
CD2 A:HIS290 3.1 18.8 1.0
CB A:HIS240 3.4 12.7 1.0
CA A:HIS240 3.9 13.2 1.0
ND1 A:HIS291 4.1 15.8 1.0
ND1 A:HIS290 4.1 19.9 1.0
CG A:HIS291 4.1 17.0 1.0
NE2 A:HIS240 4.1 17.9 1.0
CD2 A:HIS240 4.1 16.6 1.0
CG A:HIS290 4.2 17.4 1.0
NA A:HEA602 4.5 15.6 1.0
C1A A:HEA602 4.5 17.5 1.0
C4A A:HEA602 4.7 18.7 1.0
N A:HIS240 4.7 14.8 1.0
C2A A:HEA602 4.8 23.6 1.0
C3A A:HEA602 4.9 21.2 1.0
CG2 A:VAL243 4.9 15.9 1.0
FE A:HEA602 4.9 17.1 1.0
CHA A:HEA602 4.9 13.8 1.0

Copper binding site 2 out of 6 in 7y44

Go back to Copper Binding Sites List in 7y44
Copper binding site 2 out of 6 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:19.3
occ:1.00
 CU1 B:CUA302 0.0 19.3 1.0
ND1 B:HIS161 2.0 18.1 1.0
SG B:CYS196 2.3 19.1 1.0
SG B:CYS200 2.3 18.3 1.0
SD B:MET207 2.4 20.6 1.0
CU2 B:CUA302 2.5 18.9 1.0
CE1 B:HIS161 2.9 17.9 1.0
CE B:MET207 3.1 24.6 1.0
CG B:HIS161 3.2 18.1 1.0
CB B:CYS200 3.4 16.4 1.0
CB B:CYS196 3.4 20.0 1.0
CG B:MET207 3.4 16.8 1.0
CB B:HIS161 3.7 16.5 1.0
NE2 B:HIS161 4.0 16.1 1.0
O B:GLU198 4.2 19.5 1.0
CD2 B:HIS161 4.2 17.9 1.0
CA B:HIS161 4.3 21.8 1.0
ND1 B:HIS204 4.4 17.5 1.0
O B:LEU160 4.7 16.6 1.0
CA B:HIS204 4.7 21.3 1.0
O B:HIS102 4.7 20.9 1.0
CA B:CYS196 4.7 19.7 1.0
CD1 B:TRP104 4.7 17.6 1.0
CA B:CYS200 4.8 19.1 1.0
CB B:MET207 4.8 18.7 1.0
O B:HIS204 4.9 18.1 1.0

Copper binding site 3 out of 6 in 7y44

Go back to Copper Binding Sites List in 7y44
Copper binding site 3 out of 6 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:18.9
occ:1.00
 CU2 B:CUA302 0.0 18.9 1.0
ND1 B:HIS204 2.0 17.5 1.0
SG B:CYS200 2.2 18.3 1.0
SG B:CYS196 2.3 19.1 1.0
CU1 B:CUA302 2.5 19.3 1.0
O B:GLU198 2.5 19.5 1.0
CE1 B:HIS204 2.9 18.2 1.0
CG B:HIS204 3.1 16.9 1.0
CB B:CYS196 3.3 20.0 1.0
CB B:CYS200 3.4 16.4 1.0
CB B:HIS204 3.5 18.6 1.0
C B:GLU198 3.6 19.8 1.0
CA B:HIS204 3.6 21.3 1.0
N B:CYS200 3.7 20.7 1.0
O B:HIS204 3.8 18.1 1.0
NE2 B:HIS204 4.0 21.2 1.0
C B:HIS204 4.1 17.2 1.0
ND1 B:HIS161 4.1 18.1 1.0
C B:ILE199 4.1 13.7 1.0
CA B:CYS200 4.1 19.1 1.0
CD2 B:HIS204 4.2 17.8 1.0
N B:GLU198 4.2 19.1 1.0
O B:CYS196 4.2 16.7 1.0
C B:CYS196 4.3 21.7 1.0
CA B:ILE199 4.3 23.2 1.0
SD B:MET207 4.3 20.6 1.0
N B:ILE199 4.4 17.2 1.0
CA B:CYS196 4.4 19.7 1.0
CG B:MET207 4.5 16.8 1.0
CA B:GLU198 4.5 18.9 1.0
N B:SER197 4.7 16.4 1.0
N B:HIS204 4.8 21.3 1.0
CE1 B:HIS161 4.9 17.9 1.0
O B:ILE199 5.0 19.6 1.0

Copper binding site 4 out of 6 in 7y44

Go back to Copper Binding Sites List in 7y44
Copper binding site 4 out of 6 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:18.6
occ:1.00
 NE2 N:HIS291 2.0 19.1 1.0
NE2 N:HIS290 2.0 20.7 1.0
ND1 N:HIS240 2.1 14.6 1.0
O2 N:PER606 2.1 17.8 1.0
O1 N:PER606 2.7 18.1 1.0
CE1 N:HIS291 2.9 12.0 1.0
CD2 N:HIS291 3.0 15.6 1.0
CG N:HIS240 3.0 17.0 1.0
CD2 N:HIS290 3.0 19.6 1.0
CE1 N:HIS290 3.1 24.3 1.0
CE1 N:HIS240 3.1 22.5 1.0
CB N:HIS240 3.3 17.4 1.0
CA N:HIS240 3.9 18.3 1.0
ND1 N:HIS291 4.0 18.3 1.0
CG N:HIS291 4.1 13.1 1.0
ND1 N:HIS290 4.2 17.5 1.0
CD2 N:HIS240 4.2 17.9 1.0
CG N:HIS290 4.2 23.6 1.0
NE2 N:HIS240 4.2 23.8 1.0
NA N:HEA602 4.5 18.2 1.0
C1A N:HEA602 4.5 20.8 1.0
C4A N:HEA602 4.7 24.6 1.0
N N:HIS240 4.7 18.1 1.0
C2A N:HEA602 4.8 17.8 1.0
C3A N:HEA602 4.9 17.9 1.0
FE N:HEA602 4.9 17.6 1.0
CG2 N:VAL243 5.0 13.2 1.0
CHA N:HEA602 5.0 17.0 1.0

Copper binding site 5 out of 6 in 7y44

Go back to Copper Binding Sites List in 7y44
Copper binding site 5 out of 6 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:22.8
occ:1.00
 CU1 O:CUA302 0.0 22.8 1.0
ND1 O:HIS161 2.0 21.4 1.0
SG O:CYS200 2.3 21.5 1.0
SG O:CYS196 2.3 23.8 1.0
SD O:MET207 2.5 27.1 1.0
CU2 O:CUA302 2.5 22.8 1.0
CE1 O:HIS161 2.8 22.8 1.0
CG O:HIS161 3.2 23.2 1.0
CE O:MET207 3.2 22.2 1.0
CB O:CYS200 3.3 20.9 1.0
CB O:CYS196 3.4 20.4 1.0
CG O:MET207 3.6 24.8 1.0
CB O:HIS161 3.7 27.5 1.0
NE2 O:HIS161 4.0 24.3 1.0
O O:GLU198 4.1 21.1 1.0
CA O:HIS161 4.2 24.8 1.0
CD2 O:HIS161 4.2 19.9 1.0
ND1 O:HIS204 4.5 24.3 1.0
CA O:CYS200 4.7 22.7 1.0
O O:LEU160 4.7 27.7 1.0
CA O:HIS204 4.7 26.4 1.0
O O:HIS102 4.8 26.9 1.0
CA O:CYS196 4.8 24.6 1.0
CD1 O:TRP104 4.8 20.4 1.0
O O:HIS204 4.9 24.5 1.0

Copper binding site 6 out of 6 in 7y44

Go back to Copper Binding Sites List in 7y44
Copper binding site 6 out of 6 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:22.8
occ:1.00
 CU2 O:CUA302 0.0 22.8 1.0
ND1 O:HIS204 2.0 24.3 1.0
SG O:CYS200 2.3 21.5 1.0
SG O:CYS196 2.3 23.8 1.0
CU1 O:CUA302 2.5 22.8 1.0
O O:GLU198 2.5 21.1 1.0
CE1 O:HIS204 2.9 23.4 1.0
CG O:HIS204 3.1 21.3 1.0
CB O:CYS200 3.3 20.9 1.0
CB O:CYS196 3.4 20.4 1.0
CB O:HIS204 3.5 29.1 1.0
C O:GLU198 3.5 22.3 1.0
CA O:HIS204 3.6 26.4 1.0
N O:CYS200 3.7 25.1 1.0
O O:HIS204 3.8 24.5 1.0
NE2 O:HIS204 4.1 19.7 1.0
CA O:CYS200 4.1 22.7 1.0
C O:HIS204 4.1 27.2 1.0
C O:ILE199 4.1 28.0 1.0
CD2 O:HIS204 4.2 23.4 1.0
ND1 O:HIS161 4.2 21.4 1.0
N O:GLU198 4.2 19.5 1.0
CA O:ILE199 4.3 20.6 1.0
C O:CYS196 4.3 28.1 1.0
O O:CYS196 4.3 21.2 1.0
N O:ILE199 4.3 20.4 1.0
SD O:MET207 4.4 27.1 1.0
CA O:CYS196 4.5 24.6 1.0
CA O:GLU198 4.5 20.6 1.0
N O:SER197 4.7 21.1 1.0
CG O:MET207 4.7 24.8 1.0
N O:HIS204 4.8 23.8 1.0
CE1 O:HIS161 4.9 22.8 1.0
O O:ILE199 4.9 23.1 1.0
C O:CYS200 5.0 31.9 1.0
CA O:HIS161 5.0 24.8 1.0

Reference:

K.Hirata, T.Tsukihara, H.Ago. Determination of Damage-Free Crystal Structure of An X-Ray-Sensitive Protein Using An Xfel Nature Methods V. 11 734 2014.
DOI: 10.1038/NMETH.2962
Page generated: Wed Jul 31 09:23:37 2024

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