Fluorine in the structure of The Structure of Rhinovirus 16 When Complexed With Pleconaril, An Antiviral Compound (pdb 1ncr)

The binding sites of Fluorine atom in the structure of The Structure of Rhinovirus 16 When Complexed With Pleconaril, An Antiviral Compound (pdb code 1ncr). This binding sites where shown with 5.0 Angstroms radius around Fluorine atom. The 1ncr structure was solved by Y.ZHANG, A.A.SIMPSON, C.M.BATOR, S.CHAKRAVARTY, D.C.PEVEAR, G.A.SKOCHKO, T.M.TULL, G.DIANA, M.G.ROSSMANN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.7 Space group P22121 a (A) 359.494 b (A) 343.657 c (A) 332.184 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.3 Rfree (%) 24.7 Fluorine Binding Sites: Fluorine binding site 1 out of 3 in 1ncr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Fluorine in the PDB 1ncr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Met124, A: Tyr142, A: Met143, A: Tyr144, A: Val168, A: Phe179, A: Leu217, A: W117001, conact list: Atom Atom Distance (A) F CE A:Met124 3.50 F SD A:Met124 4.66 F O A:Tyr142 3.78 F CB A:Tyr142 3.31 F C A:Tyr142 3.85 F CG A:Tyr142 4.43 F CA A:Tyr142 4.19 F N A:Met143 4.33 F C A:Met143 4.72 F CA A:Met143 4.76 F N A:Tyr144 4.69 F CB A:Val168 4.84 F CG2 A:Val168 5.00 F CZ A:Phe179 3.99 F CE1 A:Phe179 4.11 F CD1 A:Leu217 3.30 F CD2 A:Leu217 4.98 F CG A:Leu217 4.68 F F2 A:W117001 2.22 F CM4 A:W117001 1.41 F N1A A:W117001 4.35 F C3B A:W117001 4.97 F C2A A:W117001 3.79 F C4B A:W117001 4.89 F C3A A:W117001 2.15 F F3 A:W117001 2.28 F N3A A:W117001 2.41 F F1 A:W117001 0.00 F O1A A:W117001 3.50 interactive model: Fluorine binding site 2 out of 3 in 1ncr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Fluorine in the PDB 1ncr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Met124, A: Tyr142, A: Ala166, A: Ser167, A: Val168, A: Phe179, A: W117001, conact list: Atom Atom Distance (A) F CE A:Met124 4.86 F O A:Tyr142 3.62 F CB A:Tyr142 4.18 F C A:Tyr142 4.34 F CA A:Tyr142 4.92 F O A:Ala166 4.73 F C A:Ala166 5.00 F O A:Ser167 4.77 F N A:Ser167 4.94 F C A:Ser167 4.11 F CA A:Ser167 4.49 F N A:Val168 3.58 F CB A:Val168 3.16 F CG2 A:Val168 2.94 F CG1 A:Val168 4.41 F CA A:Val168 3.97 F CE2 A:Phe179 4.68 F CD1 A:Phe179 4.19 F CZ A:Phe179 3.85 F CE1 A:Phe179 3.56 F CG A:Phe179 4.97 F F2 A:W117001 0.00 F CM4 A:W117001 1.34 F N1A A:W117001 4.49 F C2A A:W117001 4.57 F C3A A:W117001 2.48 F F3 A:W117001 2.21 F N3A A:W117001 3.56 F F1 A:W117001 2.22 F O1A A:W117001 3.15 interactive model: Fluorine binding site 3 out of 3 in 1ncr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Fluorine in the PDB 1ncr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Fluorine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Tyr142, A: Met143, A: Tyr144, A: Ala166, A: Ser167, A: Val168, A: Leu217, A: W117001, conact list: Atom Atom Distance (A) F O A:Tyr142 2.65 F CB A:Tyr142 4.11 F C A:Tyr142 3.17 F CA A:Tyr142 4.26 F O A:Met143 4.37 F N A:Met143 3.46 F CB A:Met143 4.70 F C A:Met143 3.44 F CA A:Met143 3.28 F N A:Tyr144 3.15 F CB A:Tyr144 4.01 F CA A:Tyr144 4.10 F O A:Ala166 3.16 F C A:Ala166 3.89 F CB A:Ala166 4.99 F N A:Ser167 4.20 F CB A:Ser167 4.98 F C A:Ser167 4.19 F CA A:Ser167 3.78 F N A:Val168 3.97 F CB A:Val168 4.76 F CG2 A:Val168 4.80 F CA A:Val168 4.98 F CD1 A:Leu217 4.44 F F2 A:W117001 2.21 F CM4 A:W117001 1.34 F N1A A:W117001 4.22 F C2A A:W117001 4.33 F C3A A:W117001 2.28 F F3 A:W117001 0.00 F N3A A:W117001 3.38 F F1 A:W117001 2.28 F O1A A:W117001 2.90 interactive model: