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Copper in PDB 3s3d: Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization

Enzymatic activity of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization

All present enzymatic activity of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization:
1.9.3.1;

Protein crystallography data

The structure of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization, PDB code: 3s3d was solved by V.M.Luna, J.A.Fee, A.A.Deniz, C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.41 / 3.75
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.030, 110.030, 170.230, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 29.3

Other elements in 3s3d:

The structure of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Xenon (Xe) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization (pdb code 3s3d). 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 Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization, PDB code: 3s3d:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 3s3d

Go back to Copper Binding Sites List in 3s3d
Copper binding site 1 out of 3 in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu803

b:61.1
occ:1.00
ND1 A:HIS233 1.9 61.1 1.0
NE2 A:HIS283 1.9 61.1 1.0
NE2 A:HIS282 2.2 61.1 1.0
CE1 A:HIS233 2.8 61.1 1.0
CE1 A:HIS283 2.8 61.1 1.0
CG A:HIS233 2.9 61.1 1.0
CD2 A:HIS283 3.0 61.1 1.0
CE1 A:HIS282 3.1 61.1 1.0
CD2 A:HIS282 3.3 61.1 1.0
CB A:HIS233 3.4 61.1 1.0
NE2 A:HIS233 3.9 61.1 1.0
ND A:HAS801 3.9 61.1 1.0
ND1 A:HIS283 3.9 61.1 1.0
CD2 A:HIS233 4.0 61.1 1.0
CA A:HIS233 4.0 61.1 1.0
C1D A:HAS801 4.0 61.1 1.0
CG A:HIS283 4.1 61.1 1.0
ND1 A:HIS282 4.2 61.1 1.0
C4D A:HAS801 4.3 61.1 1.0
CG A:HIS282 4.3 61.1 1.0
CHB A:HAS801 4.4 61.1 1.0
FE A:HAS801 4.4 61.1 1.0
C2D A:HAS801 4.5 61.1 1.0
C3D A:HAS801 4.7 61.1 1.0
NA A:HAS801 4.7 61.1 1.0
NB A:HAS801 4.8 61.1 1.0
C1B A:HAS801 4.8 61.1 1.0
CHA A:HAS801 4.9 61.1 1.0
C A:HIS233 4.9 61.1 1.0
CG2 A:VAL236 4.9 61.1 1.0
O A:HIS233 4.9 61.1 1.0
N A:HIS233 4.9 61.1 1.0
C1A A:HAS801 5.0 61.1 1.0

Copper binding site 2 out of 3 in 3s3d

Go back to Copper Binding Sites List in 3s3d
Copper binding site 2 out of 3 in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu802

b:61.1
occ:1.00
CU1 B:CUA802 0.0 61.1 1.0
SG B:CYS153 1.9 61.1 1.0
ND1 B:HIS157 2.1 61.1 1.0
SG B:CYS149 2.3 61.1 1.0
O B:GLN151 2.6 61.1 1.0
CU2 B:CUA802 2.7 61.1 1.0
CG B:HIS157 3.0 61.1 1.0
CE1 B:HIS157 3.1 61.1 1.0
CB B:CYS153 3.2 61.1 1.0
CB B:HIS157 3.3 61.1 1.0
N B:CYS153 3.4 61.1 1.0
CB B:CYS149 3.4 61.1 1.0
C B:GLN151 3.6 61.1 1.0
CA B:HIS157 3.8 61.1 1.0
CA B:CYS153 3.9 61.1 1.0
C B:TYR152 4.1 61.1 1.0
NE2 B:HIS157 4.2 61.1 1.0
CD2 B:HIS157 4.2 61.1 1.0
O B:HIS157 4.2 61.1 1.0
ND1 B:HIS114 4.2 61.1 1.0
CA B:TYR152 4.2 61.1 1.0
N B:TYR152 4.3 61.1 1.0
N B:GLN151 4.4 61.1 1.0
SD B:MET160 4.4 61.1 1.0
C B:HIS157 4.4 61.1 1.0
O B:CYS149 4.4 61.1 1.0
C B:CYS149 4.4 61.1 1.0
CA B:CYS149 4.5 61.1 1.0
CA B:GLN151 4.7 61.1 1.0
CB B:MET160 4.8 61.1 1.0
C B:CYS153 4.9 61.1 1.0
CE1 B:HIS114 5.0 61.1 1.0
O B:TYR152 5.0 61.1 1.0

Copper binding site 3 out of 3 in 3s3d

Go back to Copper Binding Sites List in 3s3d
Copper binding site 3 out of 3 in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu802

b:61.1
occ:1.00
CU2 B:CUA802 0.0 61.1 1.0
ND1 B:HIS114 1.8 61.1 1.0
SG B:CYS153 2.2 61.1 1.0
SD B:MET160 2.3 61.1 1.0
SG B:CYS149 2.3 61.1 1.0
CU1 B:CUA802 2.7 61.1 1.0
CE1 B:HIS114 2.7 61.1 1.0
CG B:HIS114 3.0 61.1 1.0
CB B:CYS153 3.1 61.1 1.0
CE B:MET160 3.3 61.1 1.0
CB B:HIS114 3.4 61.1 1.0
CB B:CYS149 3.5 61.1 1.0
CG B:MET160 3.8 61.1 1.0
NE2 B:HIS114 3.9 61.1 1.0
CA B:HIS114 4.0 61.1 1.0
CD2 B:HIS114 4.0 61.1 1.0
CB B:MET160 4.1 61.1 1.0
O B:GLN151 4.3 61.1 1.0
CA B:CYS153 4.6 61.1 1.0
ND1 B:HIS157 4.7 61.1 1.0
O B:ILE113 4.8 61.1 1.0
O B:PHE86 4.8 61.1 1.0
CA B:CYS149 4.8 61.1 1.0
N B:CYS153 4.9 61.1 1.0
N B:GLY115 4.9 61.1 1.0
N B:PHE88 4.9 61.1 1.0

Reference:

V.M.Luna, J.A.Fee, A.A.Deniz, C.D.Stout. Mobility of Xe Atoms Within the Oxygen Diffusion Channel of Cytochrome Ba(3) Oxidase. Biochemistry V. 51 4669 2012.
ISSN: ISSN 0006-2960
PubMed: 22607023
DOI: 10.1021/BI3003988
Page generated: Sun Dec 13 11:11:47 2020

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