Yttrium in the structure of Structure of the Dnag Catalytic Core (pdb 1dde)

The binding sites of Yttrium atom in the structure of Structure of the Dnag Catalytic Core (pdb code 1dde). This binding sites where shown with 5.0 Angstroms radius around Yttrium atom. The 1dde structure was solved by J.L.KECK, D.D.ROCHE, A.S.LYNCH, J.M.BERGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.7 Space group P212121 a (A) 38.020 b (A) 55.890 c (A) 139.490 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.9 Rfree (%) 26.3 Yttrium Binding Sites: Yttrium binding site 1 out of 4 in 1dde Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Yttrium in the PDB 1dde. 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: Asp331, A: Glu405, A: Thr406, A: Hoh445, A: Hoh457, A: Hoh528, A: Hoh535, A: Hoh582, A: Hoh613, A: Hoh619, conact list: Atom Atom Distance (A) Y CB A:Asp331 3.64 Y OD2 A:Asp331 2.31 Y OD1 A:Asp331 4.45 Y CG A:Asp331 3.32 Y N A:Glu405 4.58 Y OE1 A:Glu405 2.54 Y OE2 A:Glu405 2.48 Y CD A:Glu405 2.95 Y CG A:Glu405 4.43 Y N A:Thr406 4.67 Y CB A:Thr406 4.89 Y OG1 A:Thr406 4.15 Y O A:Hoh445 2.67 Y O A:Hoh457 2.89 Y O A:Hoh528 2.59 Y O A:Hoh535 2.83 Y O A:Hoh582 4.51 Y O A:Hoh613 4.53 Y O A:Hoh619 4.96 interactive model: Yttrium binding site 2 out of 4 in 1dde Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Yttrium in the PDB 1dde. 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: Glu265, A: Asp309, A: Asp311, A: Y13, A: Y14, A: Hoh559, A: Hoh596, A: Hoh604, conact list: Atom Atom Distance (A) Y OE1 A:Glu265 2.55 Y CB A:Glu265 4.52 Y OE2 A:Glu265 4.03 Y CD A:Glu265 3.54 Y CG A:Glu265 4.65 Y CB A:Asp309 4.40 Y OD2 A:Asp309 3.03 Y CG A:Asp309 4.13 Y OD2 A:Asp311 4.23 Y OD1 A:Asp311 4.76 Y CG A:Asp311 4.91 Y Y A:Y13 1.89 Y Y A:Y14 2.51 Y O A:Hoh559 3.96 Y O A:Hoh596 3.24 Y O A:Hoh604 4.44 interactive model: Yttrium binding site 3 out of 4 in 1dde Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Yttrium in the PDB 1dde. 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: Glu265, A: Asp309, A: Asp311, A: Ala313, A: Y12, A: Y14, A: Hoh559, A: Hoh596, A: Hoh699, conact list: Atom Atom Distance (A) Y OE1 A:Glu265 2.41 Y CB A:Glu265 4.92 Y OE2 A:Glu265 3.91 Y CD A:Glu265 3.49 Y CG A:Glu265 4.75 Y OD2 A:Asp309 4.39 Y OD2 A:Asp311 4.37 Y OD1 A:Asp311 4.53 Y CG A:Asp311 4.93 Y CB A:Ala313 4.72 Y Y A:Y12 1.89 Y Y A:Y14 4.21 Y O A:Hoh559 4.97 Y O A:Hoh596 2.84 Y O A:Hoh699 4.43 interactive model: Yttrium binding site 4 out of 4 in 1dde Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Yttrium in the PDB 1dde. 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: Glu265, A: Asp309, A: Asp311, A: Glu344, A: Asp345, A: Y12, A: Y13, A: Hoh559, A: Hoh585, A: Hoh596, A: Hoh604, A: Hoh643, conact list: Atom Atom Distance (A) Y OE1 A:Glu265 4.23 Y OE2 A:Glu265 4.73 Y CD A:Glu265 4.64 Y CB A:Asp309 3.00 Y OD2 A:Asp309 2.43 Y OD1 A:Asp309 4.14 Y CG A:Asp309 3.04 Y CA A:Asp309 4.50 Y OD2 A:Asp311 4.03 Y OD1 A:Asp311 4.73 Y CG A:Asp311 4.57 Y O A:Glu344 4.82 Y CB A:Asp345 4.41 Y OD2 A:Asp345 4.86 Y Y A:Y12 2.51 Y Y A:Y13 4.21 Y O A:Hoh559 3.04 Y O A:Hoh585 3.01 Y O A:Hoh596 3.98 Y O A:Hoh604 4.12 Y O A:Hoh643 4.55 interactive model: