Xenon in PDB 3s3d: 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;

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

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

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

The binding sites of Xenon 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 Xenon atom.
In total 3 binding sites of Xenon where determined in the Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 480S After Xe Depressurization, PDB code: 3s3d:
Jump to Xenon binding site number: 1; 2; 3;

Xenon 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 Xenon with other atoms in the Xe 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:Xe563 b:61.1 occ:0.31 CE2 A:TYR133 3.4 61.1 1.0 OH A:TYR133 3.7 61.1 1.0 O A:GLY232 3.8 61.1 1.0 CZ A:TYR133 3.9 61.1 1.0 CZ3 A:TRP229 4.0 61.1 1.0 CG2 A:ILE235 4.1 61.1 1.0 CH2 A:TRP229 4.1 61.1 1.0 CD2 A:TYR133 4.3 61.1 1.0 CH2 A:TRP239 4.4 61.1 1.0 CZ A:PHE228 4.5 61.1 1.0 CZ2 A:TRP239 4.6 61.1 1.0 CE2 A:PHE228 4.7 61.1 1.0 CA A:GLY232 4.7 61.1 1.0 C A:GLY232 4.7 61.1 1.0 CBA A:HAS801 4.8 61.1 1.0

Xenon 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 Xenon with other atoms in the Xe 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 A:Xe564 b:61.1 occ:0.40 CG A:PHE152 4.0 61.1 1.0 CA A:ALA149 4.0 61.1 1.0 CB A:PHE152 4.1 61.1 1.0 CD2 A:PHE152 4.2 61.1 1.0 CB A:ALA149 4.2 61.1 1.0 CG2 A:VAL79 4.2 61.1 1.0 CG1 A:VAL74 4.2 61.1 1.0 CB A:ALA120 4.3 61.1 1.0 CG2 A:ILE78 4.4 61.1 1.0 CD1 A:PHE152 4.5 61.1 1.0 N A:ALA149 4.5 61.1 1.0 O A:GLY116 4.8 61.1 1.0 CE2 A:PHE152 4.8 61.1 1.0 CA A:LEU117 4.8 61.1 1.0 C A:GLY148 4.9 61.1 1.0 CD1 A:LEU117 5.0 61.1 1.0 O A:GLY148 5.0 61.1 1.0

Xenon 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 Xenon with other atoms in the Xe 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 A:Xe565 b:61.1 occ:0.22 O A:TYR146 4.0 61.1 1.0 CB A:ALA149 4.0 61.1 1.0 OG A:SER150 4.0 61.1 1.0 CD1 A:LEU200 4.1 61.1 1.0 CZ A:PHE135 4.1 61.1 1.0 CB A:ALA204 4.1 61.1 1.0 CE1 A:PHE135 4.1 61.1 1.0 N A:SER150 4.3 61.1 1.0 CD1 A:LEU208 4.4 61.1 1.0 CG A:LEU200 4.6 61.1 1.0 CA A:SER150 4.6 61.1 1.0 C A:ALA149 4.7 61.1 1.0 CD2 A:TYR146 4.8 61.1 1.0 CA A:TYR146 4.8 61.1 1.0 C A:TYR146 4.8 61.1 1.0 CD2 A:LEU200 4.9 61.1 1.0 CB A:SER150 5.0 61.1 1.0 CA A:ALA149 5.0 61.1 1.0 CE2 A:PHE135 5.0 61.1 1.0

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