Silicon in the structure of Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin (pdb 1y3g)

The binding sites of Silicon atom in the structure of Crystal Structure of A Silanediol Protease Inhibitor Bound to Thermolysin (pdb code 1y3g). This binding sites where shown with 5.0 Angstroms radius around Silicon atom. The 1y3g structure was solved by D.H.JUERS, J.KIM, B.W.MATTHEWS, S.M.SIEBURTH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 31.0-2.1 Space group P6122 a (A) 93.520 b (A) 93.520 c (A) 131.770 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 15.5 Rfree (%) 22.5 Silicon Binding Sites: Silicon binding site 1 out of 1 in 1y3g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Silicon in the PDB 1y3g. 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: E: Asn112, E: Ala113, E: Phe114, E: His142, E: Glu143, E: His146, E: Tyr157, E: Glu166, E: His231, E: Zn321, E: Dms802, E: 3pl803, E: Amm804, E: Leu805, conact list: Atom Atom Distance (A) Si OD1 E:Asn112 4.41 Si O E:Ala113 3.56 Si C E:Ala113 4.56 Si CA E:Phe114 4.74 Si NE2 E:His142 4.26 Si CD2 E:His142 4.65 Si OE1 E:Glu143 4.15 Si OE2 E:Glu143 3.80 Si CD E:Glu143 4.42 Si NE2 E:His146 4.16 Si CD2 E:His146 4.56 Si OH E:Tyr157 4.30 Si OE2 E:Glu166 4.53 Si NE2 E:His231 3.79 Si CD2 E:His231 4.95 Si CE1 E:His231 4.34 Si ZN E:Zn321 3.15 Si S E:Dms802 4.75 Si O E:Dms802 3.84 Si C1 E:Dms802 4.30 Si O E:3pl803 4.58 Si C E:3pl803 4.04 Si O E:Amm804 4.31 Si SI E:Amm804 0.00 Si O2 E:Amm804 1.64 Si N E:Amm804 2.77 Si CB E:Amm804 4.23 Si CE E:Amm804 2.90 Si O1 E:Amm804 1.64 Si CH2 E:Amm804 1.85 Si C E:Amm804 3.51 Si CA E:Amm804 1.84 Si O E:Leu805 4.60 Si N E:Leu805 3.78 Si CA E:Leu805 4.91 interactive model: