Yttrium in the structure of Structure of The GP41 N-Peptide in Complex With the Hiv Entry Inhibitor PIE1 (pdb 2r3c)

The binding sites of Yttrium atom in the structure of Structure of The GP41 N-Peptide in Complex With the Hiv Entry Inhibitor PIE1 (pdb code 2r3c). This binding sites where shown with 5.0 Angstroms radius around Yttrium atom. The 2r3c structure was solved by A.P.VANDEMARK, B.WELCH, A.HEROUX, C.P.HILL, M.S.KAY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.7 Space group P63 a (A) 46.843 b (A) 46.843 c (A) 137.079 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.3 Rfree (%) 23 Yttrium Binding Sites: Yttrium binding site 1 out of 5 in 2r3c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Yttrium in the PDB 2r3c. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp7, A: Glu10, C: Dgl9, A: Hoh617, A: Hoh635, A: Hoh639, C: Hoh24, C: Hoh30, C: Hoh36, conact list: Atom Atom Distance (A) Y CB A:Asp7 4.94 Y OD2 A:Asp7 2.78 Y OD1 A:Asp7 4.64 Y CG A:Asp7 3.95 Y CA A:Asp7 4.80 Y OE1 A:Glu10 2.51 Y OE2 A:Glu10 2.42 Y CD A:Glu10 2.80 Y CG A:Glu10 4.32 Y OE1 C:Dgl9 2.53 Y OE2 C:Dgl9 2.41 Y CD C:Dgl9 2.81 Y CG C:Dgl9 4.32 Y O A:Hoh617 4.74 Y O A:Hoh635 2.53 Y O A:Hoh639 4.62 Y O C:Hoh24 2.53 Y O C:Hoh30 2.34 Y O C:Hoh36 4.70 interactive model: Yttrium binding site 2 out of 5 in 2r3c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Yttrium in the PDB 2r3c. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gln16, A: Ile19, conact list: Atom Atom Distance (A) Y OE1 A:Gln16 3.43 Y CB A:Gln16 4.35 Y CD A:Gln16 4.04 Y CG A:Gln16 3.76 Y CA A:Gln16 4.53 Y CD1 A:Ile19 4.16 interactive model: Yttrium binding site 3 out of 5 in 2r3c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Yttrium in the PDB 2r3c. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp7, B: Glu10, D: Dgl9, B: Hoh510, B: Hoh522, B: Hoh526, B: Hoh539, B: Hoh579, D: Hoh29, D: Hoh33, conact list: Atom Atom Distance (A) Y CB B:Asp7 4.42 Y OD2 B:Asp7 3.94 Y OD1 B:Asp7 2.10 Y CG B:Asp7 3.30 Y CA B:Asp7 4.48 Y OE1 B:Glu10 2.42 Y OE2 B:Glu10 2.71 Y CD B:Glu10 2.92 Y CG B:Glu10 4.43 Y OE1 D:Dgl9 2.40 Y OE2 D:Dgl9 2.30 Y CD D:Dgl9 2.68 Y CG D:Dgl9 4.20 Y O B:Hoh510 2.45 Y O B:Hoh522 4.41 Y O B:Hoh526 2.30 Y O B:Hoh539 4.63 Y O B:Hoh579 4.33 Y O D:Hoh29 2.68 Y O D:Hoh33 4.50 interactive model: Yttrium binding site 4 out of 5 in 2r3c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Yttrium in the PDB 2r3c. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Gln16, B: Ile19, conact list: Atom Atom Distance (A) Y NE2 B:Gln16 3.16 Y CB B:Gln16 4.09 Y CD B:Gln16 3.89 Y CG B:Gln16 3.63 Y CA B:Gln16 4.42 Y CD1 B:Ile19 4.39 interactive model: Yttrium binding site 5 out of 5 in 2r3c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Yttrium in the PDB 2r3c. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Leu30, B: Thr33, conact list: Atom Atom Distance (A) Y O B:Leu30 4.97 Y CD1 B:Leu30 3.62 Y CB B:Thr33 3.32 Y CG2 B:Thr33 3.66 Y OG1 B:Thr33 2.82 Y CA B:Thr33 4.81 interactive model: