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Copper in PDB 4gp5: Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W From Thermus Thermophilus

Enzymatic activity of Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W From Thermus Thermophilus

All present enzymatic activity of Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W From Thermus Thermophilus:
1.9.3.1;

Protein crystallography data

The structure of Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W From Thermus Thermophilus, PDB code: 4gp5 was solved by Y.Li, Y.Chen, C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.60 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 144.090, 97.960, 94.650, 90.00, 127.99, 90.00
R / Rfree (%) 17.3 / 23

Other elements in 4gp5:

The structure of Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W From Thermus Thermophilus also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W From Thermus Thermophilus (pdb code 4gp5). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W From Thermus Thermophilus, PDB code: 4gp5:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 4gp5

Go back to Copper Binding Sites List in 4gp5
Copper binding site 1 out of 3 in the Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W 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 Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:19.4
occ:1.00
ND1 A:HIS233 1.9 15.7 1.0
NE2 A:HIS283 2.0 19.7 1.0
NE2 A:HIS282 2.0 21.5 1.0
O2 A:PER604 2.5 22.2 1.0
O1 A:PER604 2.8 20.5 1.0
CG A:HIS233 2.8 15.8 1.0
CE1 A:HIS233 2.9 15.2 1.0
CD2 A:HIS283 2.9 20.4 1.0
CE1 A:HIS282 3.0 22.3 1.0
CE1 A:HIS283 3.0 19.3 1.0
CD2 A:HIS282 3.0 21.7 1.0
CB A:HIS233 3.1 16.6 1.0
CA A:HIS233 3.7 17.2 1.0
CD2 A:HIS233 3.9 15.6 1.0
NE2 A:HIS233 4.0 15.4 1.0
ND1 A:HIS283 4.0 19.1 1.0
CG A:HIS283 4.0 19.9 1.0
ND1 A:HIS282 4.1 23.7 1.0
CG A:HIS282 4.2 20.7 1.0
C1D A:HAS603 4.3 15.7 1.0
C4D A:HAS603 4.3 16.7 1.0
ND A:HAS603 4.4 14.9 1.0
CHB A:HAS603 4.6 13.8 1.0
N A:HIS233 4.6 17.4 1.0
C3D A:HAS603 4.6 17.6 1.0
C2D A:HAS603 4.6 19.0 1.0
C A:HIS233 4.7 18.0 1.0
O A:HIS233 4.8 18.2 1.0
CHA A:HAS603 4.8 16.2 1.0
FE A:HAS603 4.8 15.4 1.0
CG2 A:VAL236 4.9 12.2 1.0
O A:GLY232 4.9 18.2 1.0

Copper binding site 2 out of 3 in 4gp5

Go back to Copper Binding Sites List in 4gp5
Copper binding site 2 out of 3 in the Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W 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 Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:20.1
occ:1.00
CU1 B:CUA201 0.0 20.1 1.0
ND1 B:HIS157 2.0 17.8 1.0
SG B:CYS149 2.2 16.4 1.0
SG B:CYS153 2.3 19.0 1.0
O B:GLN151 2.5 17.4 1.0
CU2 B:CUA201 2.7 18.3 1.0
CE1 B:HIS157 2.9 14.3 1.0
CG B:HIS157 3.1 19.3 1.0
CB B:CYS153 3.3 19.3 1.0
CB B:CYS149 3.4 16.8 1.0
CB B:HIS157 3.5 19.8 1.0
N B:CYS153 3.5 18.9 1.0
C B:GLN151 3.5 17.6 1.0
CA B:HIS157 3.7 19.9 1.0
C B:TYR152 4.0 18.6 1.0
O B:CYS149 4.0 17.2 1.0
CA B:CYS153 4.0 19.3 1.0
NE2 B:HIS157 4.1 17.3 1.0
CA B:TYR152 4.1 17.6 1.0
CD2 B:HIS157 4.2 16.3 1.0
N B:TYR152 4.2 17.8 1.0
O B:HIS157 4.2 19.8 1.0
C B:CYS149 4.2 16.1 1.0
ND1 B:HIS114 4.4 20.9 1.0
C B:HIS157 4.4 19.7 1.0
N B:GLN151 4.4 16.3 1.0
CA B:CYS149 4.4 16.6 1.0
SD B:MET160 4.5 24.8 1.0
CA B:GLN151 4.5 17.2 1.0
O B:TYR152 4.8 19.3 1.0
N B:ASN150 4.9 15.4 1.0
N B:HIS157 4.9 20.8 1.0
CB B:MET160 4.9 19.0 1.0
C B:CYS153 5.0 19.5 1.0

Copper binding site 3 out of 3 in 4gp5

Go back to Copper Binding Sites List in 4gp5
Copper binding site 3 out of 3 in the Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W 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 Structure of Recombinant Cytochrome BA3 Oxidase Mutant Y133W From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:18.3
occ:1.00
CU2 B:CUA201 0.0 18.3 1.0
ND1 B:HIS114 2.0 20.9 1.0
SG B:CYS153 2.2 19.0 1.0
SG B:CYS149 2.2 16.4 1.0
SD B:MET160 2.3 24.8 1.0
CU1 B:CUA201 2.7 20.1 1.0
CE1 B:HIS114 2.8 21.6 1.0
CE B:MET160 3.1 21.0 1.0
CB B:CYS153 3.1 19.3 1.0
CG B:HIS114 3.2 20.0 1.0
CB B:CYS149 3.3 16.8 1.0
CB B:HIS114 3.7 19.3 1.0
CG B:MET160 3.8 19.3 1.0
NE2 B:HIS114 4.0 21.0 1.0
CA B:HIS114 4.1 19.4 1.0
O B:GLN151 4.1 17.4 1.0
CB B:MET160 4.2 19.0 1.0
CD2 B:HIS114 4.2 21.4 1.0
CA B:CYS153 4.5 19.3 1.0
ND1 B:HIS157 4.6 17.8 1.0
O B:ILE113 4.6 22.3 1.0
CA B:CYS149 4.7 16.6 1.0
CD2 B:PHE88 4.7 21.7 1.0
N B:CYS153 4.8 18.9 1.0
N B:GLY115 4.9 18.0 1.0

Reference:

W.Mcdonald, C.Funatogawa, Y.Li, I.Szundi, Y.Chen, J.A.Fee, C.D.Stout, O.Einarsdottir. Ligand Access to the Active Site in Thermus Thermophilusba(3) and Bovine Heart Aa(3) Cytochrome Oxidases. Biochemistry V. 52 640 2013.
ISSN: ISSN 0006-2960
PubMed: 23282175
DOI: 10.1021/BI301358A
Page generated: Sun Dec 13 11:14:33 2020

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