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Copper in PDB 3bvd: Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN

Enzymatic activity of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN

All present enzymatic activity of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN:
1.9.3.1;

Protein crystallography data

The structure of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN, PDB code: 3bvd was solved by V.M.Luna, Y.Chen, J.A.Fee, C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.96 / 3.37
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.726, 119.726, 153.535, 90.00, 90.00, 90.00
R / Rfree (%) 29.2 / 33.6

Other elements in 3bvd:

The structure of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Xenon (Xe) 7 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN (pdb code 3bvd). 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 Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN, PDB code: 3bvd:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 3bvd

Go back to Copper Binding Sites List in 3bvd
Copper binding site 1 out of 3 in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu803

b:85.5
occ:1.00
 ND1 A:HIS233 1.7 85.5 1.0
NE2 A:HIS282 2.0 85.5 1.0
NE2 A:HIS283 2.2 85.5 1.0
CE1 A:HIS233 2.6 85.5 1.0
CG A:HIS233 2.7 85.5 1.0
CE1 A:HIS283 2.9 85.5 1.0
CE1 A:HIS282 3.0 85.5 1.0
CD2 A:HIS282 3.0 85.5 1.0
CB A:HIS233 3.1 85.5 1.0
CD2 A:HIS283 3.2 85.5 1.0
NE2 A:HIS233 3.7 85.5 1.0
CD2 A:HIS233 3.7 85.5 1.0
CA A:HIS233 3.8 85.5 1.0
C1D A:HAS801 4.0 85.5 1.0
ND1 A:HIS283 4.1 85.5 1.0
ND A:HAS801 4.1 85.5 1.0
ND1 A:HIS282 4.1 85.5 1.0
CG A:HIS282 4.2 85.5 1.0
CG A:HIS283 4.2 85.5 1.0
C4D A:HAS801 4.4 85.5 1.0
C2D A:HAS801 4.4 85.5 1.0
CHB A:HAS801 4.4 85.5 1.0
C3D A:HAS801 4.6 85.5 1.0
FE A:HAS801 4.7 85.5 1.0
N A:HIS233 4.7 85.5 1.0
C A:HIS233 4.9 85.5 1.0
O A:HIS233 4.9 85.5 1.0
O A:GLY232 4.9 85.5 1.0
C1B A:HAS801 4.9 85.5 1.0
OMD A:HAS801 5.0 85.5 1.0

Copper binding site 2 out of 3 in 3bvd

Go back to Copper Binding Sites List in 3bvd
Copper binding site 2 out of 3 in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu802

b:85.5
occ:1.00
 CU1 B:CUA802 0.0 85.5 1.0
ND1 B:HIS157 2.0 85.5 1.0
SG B:CYS153 2.1 85.5 1.0
O B:GLN151 2.2 85.5 1.0
SG B:CYS149 2.2 85.5 1.0
CU2 B:CUA802 2.7 85.5 1.0
CE1 B:HIS157 2.9 85.5 1.0
CG B:HIS157 3.1 85.5 1.0
CB B:CYS153 3.3 85.5 1.0
C B:GLN151 3.4 85.5 1.0
N B:CYS153 3.5 85.5 1.0
CB B:CYS149 3.5 85.5 1.0
CB B:HIS157 3.6 85.5 1.0
CA B:HIS157 3.9 85.5 1.0
CA B:CYS153 4.0 85.5 1.0
NE2 B:HIS157 4.1 85.5 1.0
N B:GLN151 4.1 85.5 1.0
C B:TYR152 4.2 85.5 1.0
CD2 B:HIS157 4.2 85.5 1.0
N B:TYR152 4.2 85.5 1.0
CA B:TYR152 4.3 85.5 1.0
O B:HIS157 4.3 85.5 1.0
SD B:MET160 4.3 85.5 1.0
O B:CYS149 4.3 85.5 1.0
CA B:GLN151 4.3 85.5 1.0
C B:CYS149 4.4 85.5 1.0
C B:HIS157 4.4 85.5 1.0
ND1 B:HIS114 4.6 85.5 1.0
CA B:CYS149 4.6 85.5 1.0
CB B:MET160 4.9 85.5 1.0
N B:ASN150 4.9 85.5 1.0
CB B:GLN151 5.0 85.5 1.0
C B:CYS153 5.0 85.5 1.0

Copper binding site 3 out of 3 in 3bvd

Go back to Copper Binding Sites List in 3bvd
Copper binding site 3 out of 3 in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu802

b:85.5
occ:1.00
 CU2 B:CUA802 0.0 85.5 1.0
SD B:MET160 2.1 85.5 1.0
ND1 B:HIS114 2.3 85.5 1.0
SG B:CYS153 2.4 85.5 1.0
SG B:CYS149 2.4 85.5 1.0
CU1 B:CUA802 2.7 85.5 1.0
CE B:MET160 3.1 85.5 1.0
CG B:HIS114 3.2 85.5 1.0
CB B:CYS153 3.2 85.5 1.0
CB B:HIS114 3.3 85.5 1.0
CE1 B:HIS114 3.3 85.5 1.0
CB B:CYS149 3.4 85.5 1.0
CG B:MET160 3.6 85.5 1.0
CA B:HIS114 4.0 85.5 1.0
CB B:MET160 4.1 85.5 1.0
O B:GLN151 4.2 85.5 1.0
CD2 B:HIS114 4.3 85.5 1.0
NE2 B:HIS114 4.4 85.5 1.0
CA B:CYS153 4.6 85.5 1.0
O B:PHE86 4.7 85.5 1.0
ND1 B:HIS157 4.7 85.5 1.0
N B:GLY115 4.7 85.5 1.0
CA B:CYS149 4.9 85.5 1.0
N B:CYS153 4.9 85.5 1.0
O B:ILE113 4.9 85.5 1.0
OH B:TYR90 4.9 85.5 1.0
C B:HIS114 5.0 85.5 1.0

Reference:

V.M.Luna, Y.Chen, J.A.Fee, C.D.Stout. Crystallographic Studies of Xe and Kr Binding Within the Large Internal Cavity of Cytochrome BA3 From Thermus Thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases. Biochemistry V. 47 4657 2008.
ISSN: ISSN 0006-2960
PubMed: 18376849
DOI: 10.1021/BI800045Y
Page generated: Wed Jul 31 00:45:26 2024

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