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Copper in PDB 8ajz: Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser

Enzymatic activity of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser

All present enzymatic activity of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser:
1.9.3.1;

Protein crystallography data

The structure of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser, PDB code: 8ajz was solved by C.Safari, S.Ghosh, R.Andersson, J.Johannesson, A.V.Donoso, P.Bath, R.Bosman, P.Dahl, E.Nango, R.Tanaka, D.Zoric, E.Svensson, T.Nakane, 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) 38.70 / 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 (%) 19 / 21

Other elements in 8ajz:

The structure of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser also contains other interesting chemical elements:

Iron (Fe) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser (pdb code 8ajz). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser, PDB code: 8ajz:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 8ajz

Go back to Copper Binding Sites List in 8ajz
Copper binding site 1 out of 4 in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser


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 at 2 Milliseconds After Irradiation By A 532 Nm Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:30.6
occ:0.70
 CU A:CU601 0.0 30.6 0.7
CU A:CU601 0.3 46.4 0.3
NE2 A:HIS283 1.9 46.4 0.3
NE2 A:HIS282 2.0 43.5 0.3
ND1 A:HIS233 2.0 36.7 0.3
NE2 A:HIS282 2.1 29.0 0.7
ND1 A:HIS233 2.1 27.1 0.7
NE2 A:HIS283 2.1 27.6 0.7
C A:CMO614 2.3 43.5 0.3
O A:CMO614 2.3 28.4 0.7
O A:CMO614 2.5 35.6 0.3
CE1 A:HIS283 2.5 44.1 0.3
CE1 A:HIS282 2.8 42.3 0.3
CG A:HIS233 2.8 40.1 0.3
CG A:HIS233 3.0 26.1 0.7
CE1 A:HIS283 3.0 27.1 0.7
CE1 A:HIS282 3.0 28.2 0.7
CB A:HIS233 3.0 39.6 0.3
CE1 A:HIS233 3.1 26.2 0.7
CD2 A:HIS282 3.1 27.1 0.7
CD2 A:HIS283 3.1 44.6 0.3
CD2 A:HIS283 3.1 27.7 0.7
CD2 A:HIS282 3.1 45.1 0.3
CE1 A:HIS233 3.1 37.6 0.3
C A:CMO614 3.2 26.4 0.7
CB A:HIS233 3.3 25.8 0.7
CA A:HIS233 3.6 40.6 0.3
CA A:HIS233 3.7 25.9 0.7
ND1 A:HIS283 3.7 44.4 0.3
ND1 A:HIS282 4.0 45.4 0.3
CD2 A:HIS233 4.0 41.9 0.3
CG A:HIS283 4.0 46.7 0.3
NE2 A:HIS233 4.1 41.0 0.3
ND1 A:HIS283 4.1 26.4 0.7
ND1 A:HIS282 4.2 27.8 0.7
CG A:HIS282 4.2 46.1 0.3
O A:HOH713 4.2 25.7 0.3
CD2 A:HIS233 4.2 26.6 0.7
CG A:HIS283 4.2 26.8 0.7
NE2 A:HIS233 4.2 27.8 0.7
CG A:HIS282 4.2 26.8 0.7
C1D A:HAS603 4.3 53.9 0.3
ND A:HAS603 4.3 32.2 0.7
C1D A:HAS603 4.3 31.3 0.7
C2D A:HAS603 4.4 51.1 0.3
ND A:HAS603 4.4 48.0 0.3
C4D A:HAS603 4.4 31.2 0.7
C4D A:HAS603 4.5 44.9 0.3
C2D A:HAS603 4.5 30.3 0.7
C3D A:HAS603 4.6 45.4 0.3
N A:HIS233 4.6 34.6 1.0
C3D A:HAS603 4.7 29.9 0.7
C A:HIS233 4.7 32.1 1.0
OMD A:HAS603 4.7 62.4 0.3
CHB A:HAS603 4.7 31.1 0.7
O A:HIS233 4.8 32.4 1.0
CHB A:HAS603 4.8 47.9 0.3
O A:GLY232 4.9 29.8 1.0
FE A:HAS603 4.9 35.2 0.7
CHA A:HAS603 5.0 30.1 0.7

Copper binding site 2 out of 4 in 8ajz

Go back to Copper Binding Sites List in 8ajz
Copper binding site 2 out of 4 in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser


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 at 2 Milliseconds After Irradiation By A 532 Nm Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:46.4
occ:0.30
 CU A:CU601 0.0 46.4 0.3
CU A:CU601 0.3 30.6 0.7
NE2 A:HIS282 2.0 43.5 0.3
C A:CMO614 2.0 43.5 0.3
NE2 A:HIS283 2.0 46.4 0.3
ND1 A:HIS233 2.1 36.7 0.3
NE2 A:HIS282 2.1 29.0 0.7
O A:CMO614 2.1 28.4 0.7
ND1 A:HIS233 2.2 27.1 0.7
NE2 A:HIS283 2.2 27.6 0.7
O A:CMO614 2.3 35.6 0.3
CE1 A:HIS283 2.5 44.1 0.3
CE1 A:HIS282 2.8 42.3 0.3
CG A:HIS233 2.9 40.1 0.3
C A:CMO614 2.9 26.4 0.7
CE1 A:HIS283 3.0 27.1 0.7
CE1 A:HIS233 3.0 26.2 0.7
CE1 A:HIS233 3.1 37.6 0.3
CE1 A:HIS282 3.1 28.2 0.7
CD2 A:HIS282 3.1 27.1 0.7
CD2 A:HIS282 3.1 45.1 0.3
CG A:HIS233 3.2 26.1 0.7
CB A:HIS233 3.3 39.6 0.3
CD2 A:HIS283 3.3 27.7 0.7
CD2 A:HIS283 3.3 44.6 0.3
CB A:HIS233 3.5 25.8 0.7
ND1 A:HIS283 3.8 44.4 0.3
CA A:HIS233 3.9 40.6 0.3
CA A:HIS233 3.9 25.9 0.7
ND A:HAS603 4.0 32.2 0.7
ND1 A:HIS282 4.0 45.4 0.3
C1D A:HAS603 4.0 53.9 0.3
C1D A:HAS603 4.0 31.3 0.7
CD2 A:HIS233 4.1 41.9 0.3
NE2 A:HIS233 4.1 41.0 0.3
O A:HOH713 4.2 25.7 0.3
CG A:HIS283 4.2 46.7 0.3
ND1 A:HIS283 4.2 26.4 0.7
ND A:HAS603 4.2 48.0 0.3
CG A:HIS282 4.2 46.1 0.3
ND1 A:HIS282 4.2 27.8 0.7
NE2 A:HIS233 4.2 27.8 0.7
C4D A:HAS603 4.2 31.2 0.7
C2D A:HAS603 4.2 51.1 0.3
CG A:HIS282 4.2 26.8 0.7
CD2 A:HIS233 4.3 26.6 0.7
C4D A:HAS603 4.3 44.9 0.3
CG A:HIS283 4.3 26.8 0.7
C2D A:HAS603 4.4 30.3 0.7
C3D A:HAS603 4.4 45.4 0.3
C3D A:HAS603 4.5 29.9 0.7
CHB A:HAS603 4.5 31.1 0.7
CHB A:HAS603 4.6 47.9 0.3
OMD A:HAS603 4.6 62.4 0.3
FE A:HAS603 4.6 35.2 0.7
CHA A:HAS603 4.8 30.1 0.7
N A:HIS233 4.8 34.6 1.0
C A:HIS233 4.9 32.1 1.0
CMD A:HAS603 4.9 62.1 0.3
O A:HIS233 4.9 32.4 1.0
FE A:HAS603 4.9 49.9 0.3
C1B A:HAS603 4.9 31.9 0.7
NB A:HAS603 4.9 32.8 0.7
NA A:HAS603 5.0 31.2 0.7
C1B A:HAS603 5.0 51.5 0.3

Copper binding site 3 out of 4 in 8ajz

Go back to Copper Binding Sites List in 8ajz
Copper binding site 3 out of 4 in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser


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 at 2 Milliseconds After Irradiation By A 532 Nm Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu203

b:33.3
occ:1.00
 CU1 B:CUA203 0.0 33.3 1.0
ND1 B:HIS157 2.0 26.6 1.0
O B:GLN151 2.5 26.1 1.0
SG B:CYS149 2.5 29.5 1.0
CU2 B:CUA203 2.6 34.6 1.0
CE1 B:HIS157 2.8 27.9 1.0
SG B:CYS153 2.9 36.5 1.0
CG B:HIS157 3.1 25.6 1.0
CB B:CYS153 3.3 37.8 1.0
CB B:CYS149 3.4 31.9 1.0
C B:GLN151 3.5 27.7 1.0
CB B:HIS157 3.5 26.4 1.0
N B:CYS153 3.6 37.9 1.0
CA B:HIS157 3.8 28.1 1.0
NE2 B:HIS157 4.0 27.6 1.0
CA B:CYS153 4.1 37.6 1.0
O B:CYS149 4.1 29.9 1.0
CD2 B:HIS157 4.1 26.9 1.0
C B:TYR152 4.2 30.6 1.0
O B:HIS157 4.2 28.7 1.0
CA B:TYR152 4.2 30.3 1.0
N B:TYR152 4.2 28.8 1.0
C B:CYS149 4.3 30.9 1.0
N B:GLN151 4.3 29.4 1.0
ND1 B:HIS114 4.4 25.7 1.0
C B:HIS157 4.4 29.5 1.0
SD B:MET160 4.5 29.7 1.0
CA B:CYS149 4.5 30.5 1.0
CA B:GLN151 4.5 29.5 1.0
CB B:MET160 4.8 30.0 1.0
N B:ASN150 4.9 28.5 1.0
N B:HIS157 5.0 29.9 1.0

Copper binding site 4 out of 4 in 8ajz

Go back to Copper Binding Sites List in 8ajz
Copper binding site 4 out of 4 in the Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu203

b:34.6
occ:1.00
 CU2 B:CUA203 0.0 34.6 1.0
ND1 B:HIS114 2.1 25.7 1.0
SG B:CYS149 2.4 29.5 1.0
SD B:MET160 2.4 29.7 1.0
CU1 B:CUA203 2.6 33.3 1.0
SG B:CYS153 2.7 36.5 1.0
CE1 B:HIS114 2.9 27.1 1.0
CB B:CYS153 3.1 37.8 1.0
CG B:HIS114 3.2 28.3 1.0
CE B:MET160 3.2 28.8 1.0
CB B:CYS149 3.3 31.9 1.0
CB B:HIS114 3.6 28.6 1.0
CG B:MET160 3.8 32.6 1.0
CA B:HIS114 4.0 30.7 1.0
O B:GLN151 4.0 26.1 1.0
NE2 B:HIS114 4.1 26.0 1.0
CB B:MET160 4.2 30.0 1.0
CD2 B:HIS114 4.2 27.4 1.0
ND1 B:HIS157 4.5 26.6 1.0
CA B:CYS153 4.6 37.6 1.0
CA B:CYS149 4.7 30.5 1.0
O B:ILE113 4.7 28.9 1.0
N B:GLY115 4.8 30.8 1.0
CD1 B:PHE88 4.9 31.0 1.0
N B:CYS153 4.9 37.9 1.0

Reference:

C.Safari, S.Ghosh, R.Andersson, J.Johannesson, A.V.Donoso, P.Bath, R.Bosman, P.Dahl, E.Nango, R.Tanaka, D.Zoric, E.Svensson, T.Nakane, S.Iwata, R.Neutze, G.Branden. Serial Femtosecond Crystallography Structure of Co Bound BA3- Type Cytochrome C Oxidase at 2 Milliseconds After Irradiation By A 532 Nm Laser To Be Published.
Page generated: Wed Jul 31 09:31:32 2024

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