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Copper in PDB 8gbt: Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase

Enzymatic activity of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase

All present enzymatic activity of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase:
1.9.3.1;

Protein crystallography data

The structure of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase, PDB code: 8gbt was solved by I.Ishigami, S.-R.Yeh, D.L.Rousseau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.3, 189, 209, 90, 90, 90
R / Rfree (%) 22.3 / 26.9

Other elements in 8gbt:

The structure of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase (pdb code 8gbt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase, PDB code: 8gbt:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 8gbt

Go back to Copper Binding Sites List in 8gbt
Copper binding site 1 out of 6 in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:44.7
occ:1.00
 NE2 A:HIS291 2.0 37.0 1.0
NE2 A:HIS290 2.0 48.4 1.0
ND1 A:HIS240 2.0 35.9 1.0
C A:CMO608 2.7 33.3 1.0
CD2 A:HIS291 2.8 36.3 1.0
CD2 A:HIS290 3.0 48.3 1.0
CE1 A:HIS240 3.0 35.7 1.0
CG A:HIS240 3.0 33.9 1.0
CE1 A:HIS290 3.1 46.1 1.0
CE1 A:HIS291 3.1 36.4 1.0
O A:CMO608 3.2 36.1 1.0
CB A:HIS240 3.3 31.4 1.0
CA A:HIS240 3.9 30.8 1.0
CG A:HIS291 3.9 35.4 1.0
ND1 A:HIS291 4.0 35.0 1.0
ND1 A:HIS290 4.1 44.8 1.0
CG A:HIS290 4.1 47.0 1.0
CD2 A:HIS240 4.2 35.7 1.0
NE2 A:HIS240 4.2 37.8 1.0
O A:TRP288 4.6 37.0 1.0
N A:HIS240 4.8 30.9 1.0
NA A:HEA602 4.8 32.4 1.0
C1A A:HEA602 4.9 33.4 1.0
C A:HIS240 5.0 32.8 1.0
O A:VAL287 5.0 33.8 1.0

Copper binding site 2 out of 6 in 8gbt

Go back to Copper Binding Sites List in 8gbt
Copper binding site 2 out of 6 in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:46.4
occ:1.00
 CU1 B:CUA301 0.0 46.4 1.0
ND1 B:HIS161 2.0 37.4 1.0
SG B:CYS196 2.3 37.1 1.0
SG B:CYS200 2.3 33.2 1.0
SD B:MET207 2.4 49.6 1.0
CU2 B:CUA301 2.7 41.4 1.0
CE B:MET207 2.9 49.1 1.0
CE1 B:HIS161 3.0 34.8 1.0
CB B:CYS200 3.0 33.6 1.0
CG B:HIS161 3.1 36.3 1.0
CB B:CYS196 3.4 38.3 1.0
CB B:HIS161 3.4 38.6 1.0
CG B:MET207 3.5 49.2 1.0
O B:GLU198 4.0 41.5 1.0
CA B:HIS161 4.1 38.4 1.0
NE2 B:HIS161 4.1 33.6 1.0
CD2 B:HIS161 4.2 35.4 1.0
CA B:CYS200 4.5 32.6 1.0
ND1 B:HIS204 4.6 38.0 1.0
CD1 B:TRP104 4.7 40.5 1.0
O B:HIS102 4.7 34.5 1.0
CA B:CYS196 4.8 37.0 1.0
N B:CYS200 4.8 31.1 1.0
O B:LEU160 4.8 41.7 1.0
CB B:MET207 4.8 49.6 1.0
CZ2 B:TRP106 4.9 44.9 1.0
CA B:HIS204 4.9 36.6 1.0

Copper binding site 3 out of 6 in 8gbt

Go back to Copper Binding Sites List in 8gbt
Copper binding site 3 out of 6 in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:41.4
occ:1.00
 CU2 B:CUA301 0.0 41.4 1.0
O B:GLU198 2.0 41.5 1.0
ND1 B:HIS204 2.0 38.0 1.0
SG B:CYS200 2.3 33.2 1.0
SG B:CYS196 2.3 37.1 1.0
CU1 B:CUA301 2.7 46.4 1.0
CE1 B:HIS204 2.9 37.9 1.0
CG B:HIS204 3.0 35.5 1.0
CB B:CYS196 3.1 38.3 1.0
C B:GLU198 3.2 34.8 1.0
CB B:CYS200 3.4 33.6 1.0
CB B:HIS204 3.4 36.0 1.0
N B:CYS200 3.5 31.1 1.0
CA B:HIS204 3.6 36.6 1.0
O B:HIS204 3.8 36.3 1.0
NE2 B:HIS204 3.9 36.7 1.0
CD2 B:HIS204 4.0 36.6 1.0
N B:GLU198 4.0 35.3 1.0
CA B:CYS200 4.1 32.6 1.0
N B:ILE199 4.1 33.2 1.0
CA B:ILE199 4.1 32.5 1.0
C B:ILE199 4.2 30.4 1.0
C B:HIS204 4.2 38.6 1.0
CA B:GLU198 4.3 36.1 1.0
CA B:CYS196 4.3 37.0 1.0
C B:CYS196 4.3 36.1 1.0
ND1 B:HIS161 4.4 37.4 1.0
SD B:MET207 4.5 49.6 1.0
O B:CYS196 4.6 34.4 1.0
N B:SER197 4.7 39.0 1.0
CG B:MET207 4.7 49.2 1.0
CA B:HIS161 4.8 38.4 1.0
N B:HIS204 4.9 37.0 1.0
CB B:HIS161 5.0 38.6 1.0

Copper binding site 4 out of 6 in 8gbt

Go back to Copper Binding Sites List in 8gbt
Copper binding site 4 out of 6 in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:55.5
occ:1.00
 NE2 N:HIS291 2.0 55.4 1.0
ND1 N:HIS240 2.0 44.9 1.0
NE2 N:HIS290 2.1 47.2 1.0
C N:CMO610 2.6 56.3 1.0
CE1 N:HIS291 2.8 54.9 1.0
CE1 N:HIS290 2.9 44.9 1.0
CG N:HIS240 3.0 42.2 1.0
CE1 N:HIS240 3.0 44.5 1.0
CD2 N:HIS291 3.1 52.8 1.0
CD2 N:HIS290 3.1 44.0 1.0
CB N:HIS240 3.3 42.4 1.0
O N:CMO610 3.6 56.4 1.0
CA N:HIS240 3.9 44.4 1.0
ND1 N:HIS291 3.9 55.9 1.0
ND1 N:HIS290 4.0 41.2 1.0
CG N:HIS291 4.1 50.8 1.0
CD2 N:HIS240 4.2 42.4 1.0
CG N:HIS290 4.2 42.6 1.0
NE2 N:HIS240 4.2 45.0 1.0
N N:HIS240 4.7 42.5 1.0
CG2 N:VAL243 4.8 42.5 1.0
NA N:HEA602 4.9 36.1 1.0
O N:TRP288 4.9 45.4 1.0
CG2 N:VAL287 4.9 47.5 1.0

Copper binding site 5 out of 6 in 8gbt

Go back to Copper Binding Sites List in 8gbt
Copper binding site 5 out of 6 in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:62.0
occ:1.00
 CU1 O:CUA301 0.0 62.0 1.0
ND1 O:HIS161 2.0 65.7 1.0
SG O:CYS200 2.3 43.0 1.0
SG O:CYS196 2.3 58.3 1.0
SD O:MET207 2.3 65.5 1.0
CU2 O:CUA301 2.7 63.2 1.0
CE1 O:HIS161 2.9 68.2 1.0
CG O:HIS161 3.0 64.2 1.0
CE O:MET207 3.1 59.0 1.0
CB O:HIS161 3.4 64.1 1.0
CB O:CYS200 3.4 49.5 1.0
CG O:MET207 3.5 64.1 1.0
CB O:CYS196 3.5 60.6 1.0
O O:GLU198 4.0 72.4 1.0
NE2 O:HIS161 4.0 68.3 1.0
CA O:HIS161 4.1 61.7 1.0
CD2 O:HIS161 4.1 67.6 1.0
ND1 O:HIS204 4.6 63.6 1.0
CD1 O:TRP104 4.7 52.0 1.0
O O:LEU160 4.8 57.3 1.0
CB O:MET207 4.8 66.2 1.0
O O:HIS102 4.8 48.8 1.0
CA O:CYS200 4.8 52.7 1.0
CA O:CYS196 4.9 61.4 1.0
O O:HIS204 4.9 57.6 1.0
CA O:HIS204 5.0 58.4 1.0
CZ2 O:TRP106 5.0 65.0 1.0

Copper binding site 6 out of 6 in 8gbt

Go back to Copper Binding Sites List in 8gbt
Copper binding site 6 out of 6 in the Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Time-Resolve Sfx Structure of A Photoproduct of Carbon Monoxide Complex of Bovine Cytochrome C Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:63.2
occ:1.00
 CU2 O:CUA301 0.0 63.2 1.0
ND1 O:HIS204 2.0 63.6 1.0
O O:GLU198 2.0 72.4 1.0
SG O:CYS200 2.3 43.0 1.0
SG O:CYS196 2.3 58.3 1.0
CU1 O:CUA301 2.7 62.0 1.0
CE1 O:HIS204 2.8 65.2 1.0
CG O:HIS204 3.1 61.7 1.0
C O:GLU198 3.3 51.8 1.0
CB O:CYS196 3.4 60.6 1.0
CB O:HIS204 3.6 59.2 1.0
CA O:HIS204 3.7 58.4 1.0
O O:HIS204 3.7 57.6 1.0
CB O:CYS200 3.8 49.5 1.0
N O:CYS200 3.9 57.2 1.0
NE2 O:HIS204 3.9 67.5 1.0
O O:CYS196 4.0 52.7 1.0
C O:HIS204 4.1 58.6 1.0
CD2 O:HIS204 4.1 64.4 1.0
N O:GLU198 4.1 55.9 1.0
C O:CYS196 4.1 60.2 1.0
N O:ILE199 4.1 50.4 1.0
CA O:ILE199 4.2 51.8 1.0
ND1 O:HIS161 4.3 65.7 1.0
C O:ILE199 4.3 57.3 1.0
CA O:GLU198 4.3 51.7 1.0
CA O:CYS196 4.4 61.4 1.0
SD O:MET207 4.5 65.5 1.0
CA O:CYS200 4.5 52.7 1.0
CG O:MET207 4.6 64.1 1.0
N O:SER197 4.7 62.5 1.0

Reference:

I.Ishigami, S.-R.Yeh, D.L.Rousseau. Detection of A Geminate Photoproduct of Bovine Cytochrome C Oxidase By Time-Resolved Serial Femtosecond Crystallography To Be Published.
Page generated: Thu Dec 28 03:51:22 2023

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