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Xenon in PDB 3s39: Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization

Enzymatic activity of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization

All present enzymatic activity of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization:
1.9.3.1;

Protein crystallography data

The structure of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization, PDB code: 3s39 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) 56.80 / 4.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.610, 113.610, 176.550, 90.00, 90.00, 90.00
R / Rfree (%) 31.5 / 34.1

Other elements in 3s39:

The structure of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Copper (Cu) 3 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization (pdb code 3s39). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 4 binding sites of Xenon where determined in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization, PDB code: 3s39:
Jump to Xenon binding site number: 1; 2; 3; 4;

Xenon binding site 1 out of 4 in 3s39

Go back to Xenon Binding Sites List in 3s39
Xenon binding site 1 out of 4 in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe563

b:0.2
occ:0.81
 CE2 A:TYR133 3.9 0.2 1.0
CG2 A:ILE235 3.9 0.2 1.0
O A:GLY232 4.0 0.2 1.0
CZ A:PHE228 4.1 0.2 1.0
OH A:TYR133 4.2 0.2 1.0
CZ A:TYR133 4.2 0.2 1.0
CZ3 A:TRP229 4.2 0.2 1.0
CE2 A:PHE228 4.3 0.2 1.0
CH2 A:TRP239 4.3 0.2 1.0
CH2 A:TRP229 4.4 0.2 1.0
CZ2 A:TRP239 4.4 0.2 1.0
CA A:GLY232 4.5 0.2 1.0
CD2 A:TYR133 4.6 0.2 1.0
C A:GLY232 4.7 0.2 1.0
CBA A:HAS801 5.0 0.2 1.0

Xenon binding site 2 out of 4 in 3s39

Go back to Xenon Binding Sites List in 3s39
Xenon binding site 2 out of 4 in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe564

b:0.2
occ:0.56
 CG2 A:VAL79 3.9 0.2 1.0
CD2 A:PHE152 4.0 0.2 1.0
CG A:PHE152 4.1 0.2 1.0
CB A:ALA120 4.2 0.2 1.0
CB A:PHE152 4.3 0.2 1.0
CG1 A:VAL74 4.3 0.2 1.0
CA A:ALA149 4.3 0.2 1.0
CD1 A:LEU117 4.4 0.2 1.0
CE2 A:PHE152 4.6 0.2 1.0
CG2 A:ILE78 4.6 0.2 1.0
CB A:ALA149 4.6 0.2 1.0
CA A:LEU117 4.7 0.2 1.0
N A:ALA149 4.7 0.2 1.0
O A:GLY116 4.8 0.2 1.0
CD1 A:PHE152 4.9 0.2 1.0

Xenon binding site 3 out of 4 in 3s39

Go back to Xenon Binding Sites List in 3s39
Xenon binding site 3 out of 4 in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe565

b:0.2
occ:0.39
 OG A:SER150 3.9 0.2 1.0
O A:TYR146 3.9 0.2 1.0
CD1 A:LEU208 3.9 0.2 1.0
CB A:ALA149 4.0 0.2 1.0
CB A:ALA204 4.0 0.2 1.0
N A:SER150 4.4 0.2 1.0
CD1 A:LEU200 4.4 0.2 1.0
CZ A:PHE135 4.4 0.2 1.0
CE1 A:PHE135 4.4 0.2 1.0
CA A:TYR146 4.6 0.2 1.0
CD2 A:TYR146 4.6 0.2 1.0
C A:TYR146 4.7 0.2 1.0
CA A:SER150 4.7 0.2 1.0
C A:ALA149 4.8 0.2 1.0
CG A:LEU200 4.8 0.2 1.0
XE A:XE566 4.9 0.2 0.2
CB A:TYR146 4.9 0.2 1.0
CA A:ALA204 4.9 0.2 1.0
CB A:SER150 4.9 0.2 1.0

Xenon binding site 4 out of 4 in 3s39

Go back to Xenon Binding Sites List in 3s39
Xenon binding site 4 out of 4 in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe566

b:0.2
occ:0.16
 CG A:LEU200 3.9 0.2 1.0
CD2 A:LEU200 3.9 0.2 1.0
CG1 A:VAL153 4.0 0.2 1.0
CB A:VAL153 4.0 0.2 1.0
CA A:VAL201 4.0 0.2 1.0
CG2 A:VAL201 4.0 0.2 1.0
CA A:SER150 4.1 0.2 1.0
N A:VAL201 4.2 0.2 1.0
O A:SER150 4.2 0.2 1.0
C A:LEU200 4.4 0.2 1.0
CB A:ALA204 4.5 0.2 1.0
O A:LEU200 4.5 0.2 1.0
CG2 A:VAL153 4.6 0.2 1.0
CB A:SER150 4.6 0.2 1.0
CB A:LEU200 4.6 0.2 1.0
CB A:VAL201 4.6 0.2 1.0
C A:SER150 4.6 0.2 1.0
OG A:SER150 4.7 0.2 1.0
XE A:XE565 4.9 0.2 0.4

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: Wed Dec 16 02:40:00 2020

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