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Copper in PDB 8k65: Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation

Enzymatic activity of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation

All present enzymatic activity of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation:
7.1.1.9;

Protein crystallography data

The structure of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation, PDB code: 8k65 was solved by C.Safari, S.Ghosh, R.Andersson, J.Johannesson, A.V.Donoso, P.Bath, D.Zoric, E.Sandelin, E.Nango, R.Tanaka, S.Iwata, R.Neutze, G.Branden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.20 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.85, 100.32, 96.62, 90, 126.76, 90
R / Rfree (%) 17 / 19.6

Other elements in 8k65:

The structure of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation (pdb code 8k65). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation, PDB code: 8k65:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 8k65

Go back to Copper Binding Sites List in 8k65
Copper binding site 1 out of 3 in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:29.0
occ:1.00
 NE2 A:HIS282 2.1 27.1 1.0
ND1 A:HIS233 2.1 26.1 1.0
NE2 A:HIS283 2.1 24.1 1.0
O A:CMO614 2.3 26.8 1.0
CG A:HIS233 3.0 24.3 1.0
CE1 A:HIS233 3.0 23.5 1.0
CE1 A:HIS282 3.0 25.3 1.0
CE1 A:HIS283 3.0 23.2 1.0
CD2 A:HIS282 3.1 23.7 1.0
CD2 A:HIS283 3.1 25.9 1.0
C A:CMO614 3.2 20.9 1.0
CB A:HIS233 3.3 24.9 1.0
CA A:HIS233 3.7 25.9 1.0
ND1 A:HIS282 4.1 25.3 1.0
CD2 A:HIS233 4.1 26.8 1.0
NE2 A:HIS233 4.2 27.2 1.0
ND1 A:HIS283 4.2 21.6 1.0
CG A:HIS282 4.2 24.3 1.0
CG A:HIS283 4.2 23.1 1.0
ND A:HAS603 4.3 27.0 1.0
C1D A:HAS603 4.3 24.1 1.0
C4D A:HAS603 4.5 24.8 1.0
C2D A:HAS603 4.5 22.7 1.0
N A:HIS233 4.6 26.4 1.0
C3D A:HAS603 4.7 22.4 1.0
CHB A:HAS603 4.7 23.5 1.0
C A:HIS233 4.7 23.2 1.0
O A:HIS233 4.8 21.8 1.0
O A:GLY232 4.8 25.4 1.0
FE A:HAS603 4.9 30.4 1.0

Copper binding site 2 out of 3 in 8k65

Go back to Copper Binding Sites List in 8k65
Copper binding site 2 out of 3 in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:25.4
occ:1.00
 CU1 B:CUA202 0.0 25.4 1.0
ND1 B:HIS157 2.0 21.4 1.0
O B:GLN151 2.3 22.7 1.0
SG B:CYS153 2.3 23.8 1.0
SG B:CYS149 2.3 23.2 1.0
CU2 B:CUA202 2.6 26.1 1.0
CE1 B:HIS157 2.8 22.8 1.0
CG B:HIS157 3.1 20.6 1.0
CB B:CYS153 3.3 24.4 1.0
CB B:CYS149 3.4 23.3 1.0
C B:GLN151 3.5 20.3 1.0
CB B:HIS157 3.5 20.3 1.0
N B:CYS153 3.6 24.3 1.0
CA B:HIS157 3.8 22.4 1.0
NE2 B:HIS157 4.0 20.6 1.0
CA B:CYS153 4.1 23.6 1.0
CD2 B:HIS157 4.1 22.5 1.0
C B:TYR152 4.2 24.9 1.0
O B:CYS149 4.2 22.6 1.0
O B:HIS157 4.2 22.5 1.0
CA B:TYR152 4.2 24.4 1.0
N B:TYR152 4.2 23.3 1.0
N B:GLN151 4.3 24.5 1.0
C B:CYS149 4.3 22.8 1.0
ND1 B:HIS114 4.4 22.8 1.0
SD B:MET160 4.4 23.7 1.0
C B:HIS157 4.4 22.4 1.0
CA B:CYS149 4.5 22.5 1.0
CA B:GLN151 4.5 22.9 1.0
CB B:MET160 4.8 23.0 1.0
N B:ASN150 4.9 22.1 1.0
N B:HIS157 5.0 24.6 1.0

Copper binding site 3 out of 3 in 8k65

Go back to Copper Binding Sites List in 8k65
Copper binding site 3 out of 3 in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:26.1
occ:1.00
 CU2 B:CUA202 0.0 26.1 1.0
ND1 B:HIS114 2.1 22.8 1.0
SG B:CYS149 2.3 23.2 1.0
SG B:CYS153 2.4 23.8 1.0
SD B:MET160 2.4 23.7 1.0
CU1 B:CUA202 2.6 25.4 1.0
CE1 B:HIS114 3.0 23.3 1.0
CG B:HIS114 3.2 23.6 1.0
CB B:CYS153 3.2 24.4 1.0
CE B:MET160 3.2 25.8 1.0
CB B:CYS149 3.4 23.3 1.0
CB B:HIS114 3.6 24.2 1.0
CG B:MET160 3.8 25.8 1.0
O B:GLN151 3.9 22.7 1.0
CA B:HIS114 4.0 25.4 1.0
NE2 B:HIS114 4.1 23.6 1.0
CB B:MET160 4.2 23.0 1.0
CD2 B:HIS114 4.3 23.2 1.0
ND1 B:HIS157 4.5 21.4 1.0
CA B:CYS153 4.6 23.6 1.0
O B:ILE113 4.7 23.4 1.0
CA B:CYS149 4.7 22.5 1.0
N B:GLY115 4.7 21.5 1.0
CD1 B:PHE88 4.8 25.5 1.0
N B:CYS153 5.0 24.3 1.0
C B:HIS114 5.0 26.6 1.0

Reference:

C.Safari, S.Ghosh, R.Andersson, J.Johannesson, A.V.Donoso, P.Bath, D.Zoric, E.Sandelin, E.Nango, R.Tanaka, S.Iwata, R.Neutze, G.Branden. Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase Without Pump Laser Irradiation To Be Published.
Page generated: Thu Dec 28 03:52:09 2023

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