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Copper in PDB 3s8f: 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment

Enzymatic activity of 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment

All present enzymatic activity of 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment:
1.9.3.1;

Protein crystallography data

The structure of 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment, PDB code: 3s8f was solved by T.Tiefenbrunn, W.Liu, Y.Chen, V.Katritch, C.D.Stout, J.A.Fee, V.Cherezov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.26 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.585, 97.816, 94.952, 90.00, 128.30, 90.00
R / Rfree (%) 18.4 / 21.5

Other elements in 3s8f:

The structure of 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment (pdb code 3s8f). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment, PDB code: 3s8f:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 3s8f

Go back to Copper Binding Sites List in 3s8f
Copper binding site 1 out of 3 in the 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu803

b:23.0
occ:1.00
NE2 A:HIS283 1.9 25.8 1.0
ND1 A:HIS233 1.9 16.1 1.0
NE2 A:HIS282 2.0 22.4 1.0
O2 A:PER563 2.3 19.4 1.0
O1 A:PER563 2.8 21.1 1.0
CG A:HIS233 2.8 22.3 1.0
CE1 A:HIS283 2.9 23.2 1.0
CE1 A:HIS282 2.9 22.9 1.0
CD2 A:HIS283 2.9 29.2 1.0
CE1 A:HIS233 3.0 21.2 1.0
CD2 A:HIS282 3.0 25.5 1.0
CB A:HIS233 3.1 21.7 1.0
CA A:HIS233 3.6 21.8 1.0
CD2 A:HIS233 4.0 21.1 1.0
ND1 A:HIS283 4.0 23.2 1.0
NE2 A:HIS233 4.1 20.0 1.0
CG A:HIS283 4.1 23.4 1.0
ND1 A:HIS282 4.1 23.3 1.0
CG A:HIS282 4.2 24.3 1.0
C1D A:HAS801 4.4 21.9 1.0
ND A:HAS801 4.4 19.5 1.0
N A:HIS233 4.5 23.5 1.0
C A:HIS233 4.6 23.9 1.0
C2D A:HAS801 4.6 23.7 1.0
C4D A:HAS801 4.6 20.2 1.0
O A:HIS233 4.7 23.7 1.0
C3D A:HAS801 4.7 23.5 1.0
O A:GLY232 4.7 24.2 1.0
CHB A:HAS801 4.8 17.9 1.0
FE A:HAS801 4.9 20.4 1.0
CMD A:HAS801 5.0 22.7 1.0

Copper binding site 2 out of 3 in 3s8f

Go back to Copper Binding Sites List in 3s8f
Copper binding site 2 out of 3 in the 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu802

b:21.2
occ:1.00
CU1 B:CUA802 0.0 21.2 1.0
ND1 B:HIS157 1.9 14.7 1.0
SG B:CYS149 2.3 20.3 1.0
SG B:CYS153 2.4 21.3 1.0
CU2 B:CUA802 2.5 20.9 1.0
O B:GLN151 2.6 19.1 1.0
CE1 B:HIS157 2.9 17.7 1.0
CG B:HIS157 3.0 14.4 1.0
CB B:CYS149 3.4 18.5 1.0
CB B:CYS153 3.5 23.5 1.0
C B:GLN151 3.5 17.2 1.0
CB B:HIS157 3.5 19.0 1.0
N B:CYS153 3.5 21.2 1.0
CA B:HIS157 3.7 21.0 1.0
NE2 B:HIS157 4.0 22.3 1.0
CA B:TYR152 4.1 21.9 1.0
C B:TYR152 4.1 21.5 1.0
CD2 B:HIS157 4.1 18.1 1.0
CA B:CYS153 4.1 22.2 1.0
O B:CYS149 4.1 18.3 1.0
N B:TYR152 4.1 19.7 1.0
O B:HIS157 4.2 20.1 1.0
C B:CYS149 4.2 18.3 1.0
N B:GLN151 4.3 18.8 1.0
SD B:MET160 4.3 19.9 1.0
ND1 B:HIS114 4.4 20.4 1.0
CA B:CYS149 4.4 18.4 1.0
C B:HIS157 4.4 20.4 1.0
CA B:GLN151 4.5 18.2 1.0
CB B:MET160 4.7 17.9 1.0
N B:ASN150 4.9 17.5 1.0
N B:HIS157 4.9 20.1 1.0

Copper binding site 3 out of 3 in 3s8f

Go back to Copper Binding Sites List in 3s8f
Copper binding site 3 out of 3 in the 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of 1.8 A Structure of BA3 Cytochrome C Oxidase From Thermus Thermophilus in Lipid Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu802

b:20.9
occ:1.00
CU2 B:CUA802 0.0 20.9 1.0
ND1 B:HIS114 2.1 20.4 1.0
SD B:MET160 2.3 19.9 1.0
SG B:CYS149 2.4 20.3 1.0
SG B:CYS153 2.4 21.3 1.0
CU1 B:CUA802 2.5 21.2 1.0
CE1 B:HIS114 2.9 20.4 1.0
CE B:MET160 3.1 17.3 1.0
CB B:CYS149 3.2 18.5 1.0
CG B:HIS114 3.2 21.1 1.0
CB B:CYS153 3.2 23.5 1.0
CB B:HIS114 3.6 17.6 1.0
CG B:MET160 3.8 17.2 1.0
O B:GLN151 4.0 19.1 1.0
CA B:HIS114 4.0 20.5 1.0
CB B:MET160 4.1 17.9 1.0
NE2 B:HIS114 4.1 21.9 1.0
CD2 B:HIS114 4.3 16.2 1.0
ND1 B:HIS157 4.4 14.7 1.0
CA B:CYS153 4.6 22.2 1.0
CA B:CYS149 4.6 18.4 1.0
O B:ILE113 4.7 22.2 1.0
CD2 B:PHE88 4.8 19.0 1.0
N B:GLY115 4.8 19.9 1.0
N B:CYS153 4.8 21.2 1.0
C B:HIS114 5.0 22.3 1.0

Reference:

T.Tiefenbrunn, W.Liu, Y.Chen, V.Katritch, C.D.Stout, J.A.Fee, V.Cherezov. High Resolution Structure of the BA3 Cytochrome C Oxidase From Thermus Thermophilus in A Lipidic Environment. Plos One V. 6 22348 2011.
ISSN: ESSN 1932-6203
PubMed: 21814577
DOI: 10.1371/JOURNAL.PONE.0022348
Page generated: Wed Jul 31 01:41:42 2024

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