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Copper in PDB 3qjq: The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus

Enzymatic activity of The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus

All present enzymatic activity of The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus:
1.9.3.1;

Protein crystallography data

The structure of The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus, PDB code: 3qjq was solved by B.Liu, Y.Zhang, J.T.Sage, T.Doukov, Y.Chen, C.D.Stout, J.A.Fee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.88 / 2.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.770, 108.770, 164.600, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28.4

Other elements in 3qjq:

The structure of The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus (pdb code 3qjq). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus, PDB code: 3qjq:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 3qjq

Go back to Copper Binding Sites List in 3qjq
Copper binding site 1 out of 3 in the The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu803

b:46.9
occ:1.00
 ND1 A:HIS233 1.9 47.6 1.0
NE2 A:HIS282 2.1 35.4 1.0
NE2 A:HIS283 2.2 34.2 1.0
O A:CMO563 2.4 81.3 1.0
CE1 A:HIS282 2.5 36.8 1.0
CG A:HIS233 2.7 45.0 1.0
CE1 A:HIS283 2.8 33.5 1.0
CB A:HIS233 2.8 43.9 1.0
CE1 A:HIS233 3.0 50.2 1.0
C A:CMO563 3.2 85.8 1.0
CD2 A:HIS282 3.3 36.6 1.0
CD2 A:HIS283 3.4 34.1 1.0
CA A:HIS233 3.5 42.7 1.0
ND1 A:HIS282 3.7 36.5 1.0
CD2 A:HIS233 3.9 47.1 1.0
ND1 A:HIS283 4.0 34.1 1.0
NE2 A:HIS233 4.0 49.2 1.0
CG A:HIS282 4.1 38.5 1.0
O A:GLY232 4.1 42.0 1.0
CG A:HIS283 4.3 34.9 1.0
N A:HIS233 4.4 41.7 1.0
C A:HIS233 4.4 42.8 1.0
O A:HIS233 4.4 42.9 1.0
ND A:HAS801 4.5 43.5 1.0
C1D A:HAS801 4.6 43.1 1.0
C A:GLY232 4.7 41.9 1.0
C4D A:HAS801 4.8 42.9 1.0
CG2 A:VAL236 4.9 44.6 1.0
C2D A:HAS801 5.0 40.9 1.0

Copper binding site 2 out of 3 in 3qjq

Go back to Copper Binding Sites List in 3qjq
Copper binding site 2 out of 3 in the The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu802

b:44.8
occ:1.00
 CU1 B:CUA802 0.0 44.8 1.0
ND1 B:HIS157 2.1 42.8 1.0
SG B:CYS149 2.1 43.3 1.0
SG B:CYS153 2.3 35.8 1.0
O B:GLN151 2.5 44.1 1.0
CU2 B:CUA802 2.7 47.9 1.0
CE1 B:HIS157 3.0 42.6 1.0
CG B:HIS157 3.2 42.3 1.0
CB B:CYS149 3.2 42.2 1.0
CB B:CYS153 3.4 38.7 1.0
N B:CYS153 3.4 40.1 1.0
C B:GLN151 3.6 43.5 1.0
CB B:HIS157 3.6 41.2 1.0
O B:CYS149 3.7 42.7 1.0
CA B:HIS157 3.9 41.3 1.0
C B:TYR152 3.9 40.8 1.0
C B:CYS149 3.9 43.0 1.0
CA B:TYR152 3.9 41.0 1.0
CA B:CYS153 4.0 39.2 1.0
NE2 B:HIS157 4.1 42.9 1.0
O B:HIS157 4.2 41.4 1.0
CA B:CYS149 4.2 42.7 1.0
N B:TYR152 4.2 42.5 1.0
CD2 B:HIS157 4.2 42.6 1.0
SD B:MET160 4.4 41.0 1.0
N B:GLN151 4.4 44.4 1.0
ND1 B:HIS114 4.5 47.5 1.0
C B:HIS157 4.5 41.5 1.0
N B:ASN150 4.6 43.6 1.0
CA B:GLN151 4.7 43.5 1.0
O B:TYR152 4.7 41.4 1.0
CB B:MET160 4.8 41.7 1.0

Copper binding site 3 out of 3 in 3qjq

Go back to Copper Binding Sites List in 3qjq
Copper binding site 3 out of 3 in the The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of The Structure of and Photolytic Induced Changes of Carbon Monoxide Binding to the Cytochrome BA3-Oxidase From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu802

b:47.9
occ:1.00
 CU2 B:CUA802 0.0 47.9 1.0
SG B:CYS149 2.1 43.3 1.0
ND1 B:HIS114 2.2 47.5 1.0
SD B:MET160 2.2 41.0 1.0
SG B:CYS153 2.4 35.8 1.0
CU1 B:CUA802 2.7 44.8 1.0
CG B:HIS114 3.0 46.4 1.0
CE B:MET160 3.0 39.8 1.0
CE1 B:HIS114 3.1 48.6 1.0
CB B:CYS149 3.1 42.2 1.0
CB B:CYS153 3.2 38.7 1.0
CB B:HIS114 3.3 44.3 1.0
CG B:MET160 3.6 42.0 1.0
CA B:HIS114 4.0 43.8 1.0
CD2 B:HIS114 4.1 48.0 1.0
CB B:MET160 4.1 41.7 1.0
NE2 B:HIS114 4.2 49.2 1.0
O B:GLN151 4.2 44.1 1.0
CA B:CYS149 4.5 42.7 1.0
CA B:CYS153 4.6 39.2 1.0
ND1 B:HIS157 4.7 42.8 1.0
N B:GLY115 4.8 43.4 1.0
N B:CYS153 4.8 40.1 1.0
O B:ILE113 4.9 43.0 1.0
N B:PHE88 4.9 42.9 1.0
C B:HIS114 4.9 43.4 1.0

Reference:

B.Liu, Y.Zhang, J.T.Sage, S.M.Soltis, T.Doukov, Y.Chen, C.D.Stout, J.A.Fee. Structural Changes That Occur Upon Photolysis of the Fe(II)(A3)-Co Complex in the Cytochrome Ba(3)-Oxidase of Thermus Thermophilus: A Combined X-Ray Crystallographic and Infrared Spectral Study Demonstrates Co Binding to Cu(B). Biochim.Biophys.Acta V.1817 658 2012.
ISSN: ISSN 0006-3002
PubMed: 22226917
DOI: 10.1016/J.BBABIO.2011.12.010
Page generated: Wed Jul 31 01:37:11 2024

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