Yttrium in the structure of Crystal Structure Analysis of Clpsn With Transition Metal Ion Bound (pdb 1mbx)

The binding sites of Yttrium atom in the structure of Crystal Structure Analysis of Clpsn With Transition Metal Ion Bound (pdb code 1mbx). This binding sites where shown with 5.0 Angstroms radius around Yttrium atom. The 1mbx structure was solved by F.GUO, L.ESSER, S.K.SINGH, M.R.MAURIZI, D.XIA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.5-2.2 Space group P3121 a (A) 87.436 b (A) 87.436 c (A) 212.955 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.8 Rfree (%) 23.1 Yttrium Binding Sites: Yttrium binding site 1 out of 5 in 1mbx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Yttrium in the PDB 1mbx. 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: Arg41, A: Glu42, A: Glu45, A: Ybt211, A: Hoh215, A: Hoh253, A: Hoh258, conact list: Atom Atom Distance (A) Y NE A:Arg41 4.82 Y OE1 A:Glu42 2.62 Y OE2 A:Glu42 2.85 Y CD A:Glu42 3.07 Y CG A:Glu42 4.58 Y OE1 A:Glu45 2.40 Y CB A:Glu45 4.93 Y OE2 A:Glu45 3.70 Y CD A:Glu45 3.40 Y CG A:Glu45 4.74 Y O5 A:Ybt211 2.34 Y C1 A:Ybt211 3.34 Y O1 A:Ybt211 2.36 Y C8 A:Ybt211 3.33 Y C2 A:Ybt211 3.39 Y C6 A:Ybt211 3.28 Y N1 A:Ybt211 2.67 Y C5 A:Ybt211 3.49 Y O2 A:Ybt211 2.36 Y Y1 A:Ybt211 0.00 Y C7 A:Ybt211 3.43 Y C4 A:Ybt211 4.87 Y C3 A:Ybt211 3.38 Y O4 A:Ybt211 2.33 Y O A:Hoh215 2.28 Y O A:Hoh253 4.81 Y O A:Hoh258 4.75 interactive model: Yttrium binding site 2 out of 5 in 1mbx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Yttrium in the PDB 1mbx. 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: Glu7, D: Glu56, A: Ybt212, D: Hoh140, conact list: Atom Atom Distance (A) Y OE1 A:Glu7 2.70 Y OE2 A:Glu7 2.86 Y CD A:Glu7 3.05 Y CG A:Glu7 4.40 Y OE1 D:Glu56 3.63 Y OE2 D:Glu56 2.80 Y CD D:Glu56 3.54 Y CG D:Glu56 4.87 Y O5 A:Ybt212 2.37 Y C1 A:Ybt212 3.37 Y O1 A:Ybt212 2.40 Y C8 A:Ybt212 3.34 Y C2 A:Ybt212 3.43 Y C6 A:Ybt212 3.34 Y N1 A:Ybt212 2.69 Y C5 A:Ybt212 3.55 Y O2 A:Ybt212 2.37 Y Y1 A:Ybt212 0.00 Y C7 A:Ybt212 3.44 Y C4 A:Ybt212 4.91 Y C3 A:Ybt212 3.40 Y O4 A:Ybt212 2.38 Y O D:Hoh140 2.84 interactive model: Yttrium binding site 3 out of 5 in 1mbx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Yttrium in the PDB 1mbx. 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: Asn3, B: Gln4, B: Glu5, B: Glu102, B: Ybt212, B: Hoh250, B: Hoh262, conact list: Atom Atom Distance (A) Y CB B:Asn3 4.49 Y ND2 B:Asn3 4.25 Y OD1 B:Asn3 2.38 Y CG B:Asn3 3.50 Y CA B:Asn3 4.59 Y N B:Gln4 4.56 Y CG B:Gln4 4.93 Y OE1 B:Glu5 4.69 Y OE1 B:Glu102 3.45 Y OE2 B:Glu102 2.39 Y CD B:Glu102 3.17 Y CG B:Glu102 4.41 Y O5 B:Ybt212 2.37 Y C1 B:Ybt212 3.31 Y O1 B:Ybt212 2.38 Y C8 B:Ybt212 3.34 Y C2 B:Ybt212 3.40 Y C6 B:Ybt212 3.29 Y N1 B:Ybt212 2.66 Y C5 B:Ybt212 3.47 Y O2 B:Ybt212 2.33 Y Y1 B:Ybt212 0.00 Y C7 B:Ybt212 3.42 Y C4 B:Ybt212 4.81 Y C3 B:Ybt212 3.34 Y O4 B:Ybt212 2.38 Y O B:Hoh250 4.24 Y O B:Hoh262 4.62 interactive model: Yttrium binding site 4 out of 5 in 1mbx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Yttrium in the PDB 1mbx. 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: Arg41, B: Glu42, B: Glu45, B: Ybt213, B: Hoh218, B: Hoh241, B: Hoh272, conact list: Atom Atom Distance (A) Y NE B:Arg41 4.67 Y NH2 B:Arg41 4.82 Y OE1 B:Glu42 2.52 Y OE2 B:Glu42 2.91 Y CD B:Glu42 3.07 Y CG B:Glu42 4.57 Y CA B:Glu42 4.98 Y OE1 B:Glu45 2.55 Y CB B:Glu45 4.91 Y OE2 B:Glu45 3.82 Y CD B:Glu45 3.52 Y CG B:Glu45 4.81 Y O5 B:Ybt213 2.35 Y C1 B:Ybt213 3.37 Y O1 B:Ybt213 2.37 Y C8 B:Ybt213 3.33 Y C2 B:Ybt213 3.41 Y C6 B:Ybt213 3.27 Y N1 B:Ybt213 2.68 Y C5 B:Ybt213 3.49 Y O2 B:Ybt213 2.39 Y Y1 B:Ybt213 0.00 Y C7 B:Ybt213 3.42 Y C4 B:Ybt213 4.90 Y C3 B:Ybt213 3.42 Y O4 B:Ybt213 2.33 Y O B:Hoh218 2.44 Y O B:Hoh241 4.80 Y O B:Hoh272 4.57 interactive model: Yttrium binding site 5 out of 5 in 1mbx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Yttrium in the PDB 1mbx. 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: Glu19, D: Asn34, D: His66, D: Ybt107, conact list: Atom Atom Distance (A) Y OE1 A:Glu19 4.16 Y OE2 A:Glu19 3.85 Y CD A:Glu19 4.24 Y OD1 D:Asn34 4.17 Y NE2 D:His66 4.18 Y N D:His66 4.96 Y CB D:His66 3.18 Y ND1 D:His66 2.17 Y CD2 D:His66 4.11 Y C D:His66 4.92 Y CE1 D:His66 3.18 Y CG D:His66 2.97 Y CA D:His66 3.95 Y O5 D:Ybt107 2.35 Y C1 D:Ybt107 3.31 Y O1 D:Ybt107 2.37 Y C8 D:Ybt107 3.31 Y C2 D:Ybt107 3.38 Y C6 D:Ybt107 3.29 Y N1 D:Ybt107 2.64 Y C5 D:Ybt107 3.48 Y O2 D:Ybt107 2.34 Y Y1 D:Ybt107 0.00 Y C7 D:Ybt107 3.40 Y C4 D:Ybt107 4.86 Y C3 D:Ybt107 3.37 Y O4 D:Ybt107 2.36 interactive model: