Atomistry » Copper » PDB 7xmc-8b9r » 8ajz
Atomistry »
  Copper »
    PDB 7xmc-8b9r »
      8ajz »

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy