Silicon in the structure of Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide (pdb 2zy0)

The binding sites of Silicon atom in the structure of Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide (pdb code 2zy0). This binding sites where shown with 5.0 Angstroms radius around Silicon atom. The 2zy0 structure was solved by Y.SATO, P.ANTONY, N.ROCHEL, D.MORAS, STRUCTURAL GENOMICSCONSORTIUM FOR RESEARCH ON GENE EXPRESSION (SGCGES), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.9 Space group P212121 a (A) 64.975 b (A) 66.850 c (A) 110.793 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.7 Rfree (%) 28.9 Silicon Binding Sites: Silicon binding site 1 out of 4 in 2zy0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Silicon in the PDB 2zy0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Silicon atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ile268, A: Phe313, A: Ile345, A: Phe346, A: Cys432, A: 21p1, conact list: Atom Atom Distance (A) Si CG2 A:Ile268 4.56 Si CZ A:Phe313 4.54 Si CG2 A:Ile345 4.79 Si CD1 A:Phe346 4.80 Si SG A:Cys432 4.45 Si C9 A:21p1 2.88 Si SI1 A:21p1 0.00 Si C12 A:21p1 4.08 Si C11 A:21p1 4.63 Si C1 A:21p1 1.86 Si C8 A:21p1 1.86 Si C2 A:21p1 1.86 Si C6 A:21p1 4.32 Si C5 A:21p1 4.25 Si SI2 A:21p1 2.96 Si C7 A:21p1 2.75 Si C10 A:21p1 4.16 Si C3 A:21p1 1.87 interactive model: Silicon binding site 2 out of 4 in 2zy0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Silicon in the PDB 2zy0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Silicon atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ile268, A: Val342, A: Ile345, A: Cys432, A: Phe439, A: 21p1, conact list: Atom Atom Distance (A) Si CD1 A:Ile268 4.98 Si CG2 A:Ile268 4.36 Si CB A:Val342 4.77 Si CG2 A:Val342 4.88 Si CG1 A:Val342 4.63 Si CG2 A:Ile345 4.78 Si SG A:Cys432 4.93 Si CE2 A:Phe439 4.60 Si C9 A:21p1 4.07 Si SI1 A:21p1 2.96 Si C12 A:21p1 2.87 Si C11 A:21p1 4.14 Si C1 A:21p1 4.22 Si C8 A:21p1 2.74 Si C2 A:21p1 4.35 Si C6 A:21p1 1.86 Si C5 A:21p1 1.86 Si SI2 A:21p1 0.00 Si C7 A:21p1 1.85 Si C10 A:21p1 4.62 Si C3 A:21p1 1.87 interactive model: Silicon binding site 3 out of 4 in 2zy0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Silicon in the PDB 2zy0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Silicon atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Ile268, C: Phe313, C: Ile345, C: Phe346, C: Val349, C: Cys432, C: 21p2, conact list: Atom Atom Distance (A) Si CG2 C:Ile268 4.57 Si CZ C:Phe313 4.59 Si CG2 C:Ile345 4.95 Si CD1 C:Phe346 4.89 Si CG2 C:Val349 4.99 Si SG C:Cys432 4.60 Si C9 C:21p2 2.88 Si SI1 C:21p2 0.00 Si C12 C:21p2 4.09 Si C11 C:21p2 4.63 Si C1 C:21p2 1.86 Si C8 C:21p2 1.86 Si C2 C:21p2 1.86 Si C6 C:21p2 4.39 Si C5 C:21p2 4.20 Si SI2 C:21p2 2.97 Si C7 C:21p2 2.76 Si C10 C:21p2 4.16 Si C3 C:21p2 1.87 interactive model: Silicon binding site 4 out of 4 in 2zy0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Silicon in the PDB 2zy0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Silicon atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Ile268, C: Val342, C: Ile345, C: Cys432, C: Phe439, C: 21p2, conact list: Atom Atom Distance (A) Si CD1 C:Ile268 4.66 Si CG2 C:Ile268 4.41 Si CB C:Val342 4.95 Si CG1 C:Val342 4.88 Si CG2 C:Ile345 4.96 Si SG C:Cys432 4.95 Si CE2 C:Phe439 4.64 Si CZ C:Phe439 4.92 Si C9 C:21p2 4.09 Si SI1 C:21p2 2.97 Si C12 C:21p2 2.89 Si C11 C:21p2 4.16 Si C1 C:21p2 4.24 Si C8 C:21p2 2.75 Si C2 C:21p2 4.35 Si C6 C:21p2 1.86 Si C5 C:21p2 1.86 Si SI2 C:21p2 0.00 Si C7 C:21p2 1.86 Si C10 C:21p2 4.65 Si C3 C:21p2 1.87 interactive model: