Platinum in the structure of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 (pdb 2hr8)

The binding sites of Platinum atom in the structure of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 (pdb code 2hr8). This binding sites where shown with 5.0 Angstroms radius around Platinum atom. The 2hr8 structure was solved by H.YAMAMOTO, M.TAKETA, N.KUNISHIMA, RIKEN STRUCTURAL GENOMICS/PROTEOMICSINITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 39.3-2.8 Space group P41212 a (A) 104.581 b (A) 104.581 c (A) 139.110 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.8 Rfree (%) 24.3 Platinum Binding Sites: Platinum binding site 1 out of 5 in 2hr8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 2hr8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Met1, A: Glu77, A: Asn78, A: Asp79, conact list: Atom Atom Distance (A) Pt N A:Met1 2.56 Pt CB A:Met1 2.67 Pt CE A:Met1 3.02 Pt C A:Met1 4.37 Pt CG A:Met1 2.71 Pt SD A:Met1 2.00 Pt CA A:Met1 2.84 Pt O A:Glu77 3.28 Pt C A:Glu77 4.21 Pt CA A:Glu77 5.00 Pt O A:Asn78 4.91 Pt N A:Asn78 4.99 Pt OD1 A:Asp79 4.31 interactive model: Platinum binding site 2 out of 5 in 2hr8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Platinum in the PDB 2hr8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg173, A: Met174, conact list: Atom Atom Distance (A) Pt O A:Arg173 4.83 Pt CB A:Met174 4.09 Pt CE A:Met174 3.78 Pt CG A:Met174 3.15 Pt SD A:Met174 2.17 Pt CA A:Met174 4.22 interactive model: Platinum binding site 3 out of 5 in 2hr8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Platinum in the PDB 2hr8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp200, A: Met220, A: Glu259, conact list: Atom Atom Distance (A) Pt O A:Asp200 3.89 Pt CB A:Asp200 4.37 Pt C A:Asp200 4.71 Pt OD1 A:Asp200 4.36 Pt CG A:Asp200 4.75 Pt CA A:Asp200 4.77 Pt CB A:Met220 4.80 Pt CE A:Met220 3.95 Pt CG A:Met220 3.67 Pt SD A:Met220 2.55 Pt OE2 A:Glu259 4.16 interactive model: Platinum binding site 4 out of 5 in 2hr8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Platinum in the PDB 2hr8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Met1, B: Val2, B: Asp79, conact list: Atom Atom Distance (A) Pt N B:Met1 2.02 Pt CB B:Met1 2.73 Pt CE B:Met1 3.64 Pt C B:Met1 4.16 Pt CG B:Met1 2.73 Pt SD B:Met1 2.02 Pt CA B:Met1 2.84 Pt N B:Val2 4.43 Pt OD2 B:Asp79 3.68 Pt OD1 B:Asp79 3.55 Pt CG B:Asp79 3.93 interactive model: Platinum binding site 5 out of 5 in 2hr8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Platinum in the PDB 2hr8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Tyr138, B: Met174, B: Tyr175, B: Glu180, conact list: Atom Atom Distance (A) Pt CZ B:Tyr138 4.78 Pt OH B:Tyr138 3.86 Pt CB B:Met174 4.09 Pt CE B:Met174 3.76 Pt CG B:Met174 2.84 Pt SD B:Met174 2.09 Pt CA B:Met174 4.96 Pt O B:Tyr175 4.26 Pt OE1 B:Glu180 4.49 Pt OE2 B:Glu180 4.46 Pt CD B:Glu180 4.91 interactive model: