Xenon in the structure of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization (pdb 3s39)

The binding sites of Xenon atom in the structure of Structure of Thermus Thermophilus Cytochrome BA3 Oxidase 60S After Xe Depressurization (pdb code 3s39). This binding sites where shown with 5.0 Angstroms radius around Xenon atom. The 3s39 structure was solved by V.M.LUNA, J.A.FEE, A.A.DENIZ, C.D.STOUT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 56.8-4.8 Space group P43212 a (A) 113.610 b (A) 113.610 c (A) 176.550 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 31.5 Rfree (%) 34.1 Xenon Binding Sites: Xenon binding site 1 out of 4 in 3s39 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Xenon in the PDB 3s39. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Xenon atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Tyr133, A: Phe228, A: Trp229, A: Gly232, A: Ile235, A: Trp239, A: Has801, conact list: Atom Atom Distance (A) Xe CE2 A:Tyr133 3.89 Xe CD2 A:Tyr133 4.60 Xe CZ A:Tyr133 4.21 Xe OH A:Tyr133 4.18 Xe CE2 A:Phe228 4.27 Xe CZ A:Phe228 4.12 Xe CZ3 A:Trp229 4.23 Xe CH2 A:Trp229 4.36 Xe O A:Gly232 4.00 Xe C A:Gly232 4.70 Xe CA A:Gly232 4.53 Xe CG2 A:Ile235 3.91 Xe CZ2 A:Trp239 4.44 Xe CH2 A:Trp239 4.32 Xe CBA A:Has801 4.95 interactive model: Xenon binding site 2 out of 4 in 3s39 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Xenon in the PDB 3s39. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Xenon atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Val74, A: Ile78, A: Val79, A: Gly116, A: Leu117, A: Ala120, A: Ala149, A: Phe152, conact list: Atom Atom Distance (A) Xe CG1 A:Val74 4.27 Xe CG2 A:Ile78 4.57 Xe CG2 A:Val79 3.95 Xe O A:Gly116 4.81 Xe CD1 A:Leu117 4.41 Xe CA A:Leu117 4.72 Xe CB A:Ala120 4.20 Xe N A:Ala149 4.73 Xe CB A:Ala149 4.64 Xe CA A:Ala149 4.30 Xe CB A:Phe152 4.27 Xe CE2 A:Phe152 4.56 Xe CD1 A:Phe152 4.86 Xe CD2 A:Phe152 3.97 Xe CG A:Phe152 4.14 interactive model: Xenon binding site 3 out of 4 in 3s39 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Xenon in the PDB 3s39. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Xenon atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Phe135, A: Tyr146, A: Ala149, A: Ser150, A: Leu200, A: Ala204, A: Leu208, A: Xe566, conact list: Atom Atom Distance (A) Xe CZ A:Phe135 4.36 Xe CE1 A:Phe135 4.39 Xe O A:Tyr146 3.93 Xe CB A:Tyr146 4.88 Xe CD2 A:Tyr146 4.61 Xe C A:Tyr146 4.72 Xe CA A:Tyr146 4.60 Xe C A:Ala149 4.78 Xe CB A:Ala149 3.97 Xe N A:Ser150 4.36 Xe CB A:Ser150 4.94 Xe OG A:Ser150 3.91 Xe CA A:Ser150 4.74 Xe CD1 A:Leu200 4.36 Xe CG A:Leu200 4.79 Xe CB A:Ala204 4.02 Xe CA A:Ala204 4.94 Xe CD1 A:Leu208 3.93 Xe XE A:Xe566 4.87 interactive model: Xenon binding site 4 out of 4 in 3s39 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Xenon in the PDB 3s39. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Xenon atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ser150, A: Val153, A: Leu200, A: Val201, A: Ala204, A: Xe565, conact list: Atom Atom Distance (A) Xe O A:Ser150 4.20 Xe CB A:Ser150 4.62 Xe OG A:Ser150 4.73 Xe C A:Ser150 4.65 Xe CA A:Ser150 4.09 Xe CB A:Val153 3.99 Xe CG2 A:Val153 4.56 Xe CG1 A:Val153 3.95 Xe O A:Leu200 4.54 Xe CB A:Leu200 4.63 Xe CD2 A:Leu200 3.93 Xe C A:Leu200 4.42 Xe CG A:Leu200 3.92 Xe N A:Val201 4.15 Xe CB A:Val201 4.63 Xe CG2 A:Val201 4.05 Xe CA A:Val201 4.03 Xe CB A:Ala204 4.46 Xe XE A:Xe565 4.87 interactive model: