Calcium in the structure of Crystal Structure of Basic Winged Bean Lectin in Complex With Alpha-D- Galactose (pdb 2du0)

The binding sites of Calcium atom in the structure of Crystal Structure of Basic Winged Bean Lectin in Complex With Alpha-D- Galactose (pdb code 2du0). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 2du0 structure was solved by K.A.KULKARNI, S.KATIYAR, A.SUROLIA, M.VIJAYAN, K.SUGUNA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.7 Space group P21212 a (A) 157.552 b (A) 89.957 c (A) 73.404 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.4 Rfree (%) 24.5 Calcium Binding Sites: Calcium binding site 1 out of 4 in 2du0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 2du0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp87, A: Gly105, A: Phe107, A: Asp124, A: Phe126, A: Arg127, A: Asn128, A: Trp130, A: Asp131, A: Mn1300, A: Hoh1403, A: Hoh1404, conact list: Atom Atom Distance (A) Ca O A:Asp87 4.62 Ca OD2 A:Asp87 4.60 Ca O A:Gly105 4.68 Ca CA A:Gly105 4.46 Ca CZ A:Phe107 4.29 Ca CE1 A:Phe107 4.77 Ca CB A:Asp124 4.30 Ca OD2 A:Asp124 2.42 Ca OD1 A:Asp124 2.49 Ca CG A:Asp124 2.79 Ca O A:Phe126 2.51 Ca N A:Phe126 4.51 Ca CB A:Phe126 4.56 Ca CD2 A:Phe126 4.55 Ca C A:Phe126 3.69 Ca CA A:Phe126 4.49 Ca N A:Arg127 4.66 Ca C A:Arg127 4.81 Ca CA A:Arg127 4.72 Ca N A:Asn128 4.04 Ca CB A:Asn128 4.13 Ca ND2 A:Asn128 4.79 Ca OD1 A:Asn128 2.58 Ca CG A:Asn128 3.65 Ca CA A:Asn128 4.73 Ca CZ2 A:Trp130 4.86 Ca CE2 A:Trp130 4.97 Ca NE1 A:Trp130 4.48 Ca CB A:Asp131 4.68 Ca OD2 A:Asp131 2.35 Ca OD1 A:Asp131 3.91 Ca CG A:Asp131 3.46 Ca MN A:Mn1300 4.28 Ca O A:Hoh1403 4.24 Ca O A:Hoh1404 2.38 interactive model: Calcium binding site 2 out of 4 in 2du0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 2du0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp87, B: Gly105, B: Phe107, B: Asp124, B: Phe126, B: Arg127, B: Asn128, B: Trp130, B: Asp131, B: Mn2300, B: Hoh2403, B: Hoh2404, B: Hoh2405, conact list: Atom Atom Distance (A) Ca O B:Asp87 4.59 Ca OD2 B:Asp87 4.64 Ca O B:Gly105 4.63 Ca CA B:Gly105 4.36 Ca CZ B:Phe107 4.55 Ca CE1 B:Phe107 4.93 Ca CB B:Asp124 4.40 Ca OD2 B:Asp124 2.63 Ca OD1 B:Asp124 2.49 Ca CG B:Asp124 2.91 Ca O B:Phe126 2.32 Ca N B:Phe126 4.34 Ca CB B:Phe126 4.34 Ca CD2 B:Phe126 4.59 Ca C B:Phe126 3.49 Ca CA B:Phe126 4.28 Ca N B:Arg127 4.48 Ca C B:Arg127 4.68 Ca CA B:Arg127 4.60 Ca N B:Asn128 3.93 Ca CB B:Asn128 4.10 Ca ND2 B:Asn128 4.44 Ca OD1 B:Asn128 2.21 Ca CG B:Asn128 3.39 Ca CA B:Asn128 4.65 Ca NE1 B:Trp130 4.69 Ca CB B:Asp131 4.69 Ca OD2 B:Asp131 2.43 Ca OD1 B:Asp131 4.28 Ca CG B:Asp131 3.64 Ca MN B:Mn2300 4.32 Ca O B:Hoh2403 4.61 Ca O B:Hoh2404 2.59 Ca O B:Hoh2405 2.45 interactive model: Calcium binding site 3 out of 4 in 2du0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 2du0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asp87, C: Gly105, C: Phe107, C: Asp124, C: Phe126, C: Arg127, C: Asn128, C: Trp130, C: Asp131, C: Mn3300, C: Hoh3402, C: Hoh3403, C: Hoh3404, conact list: Atom Atom Distance (A) Ca O C:Asp87 4.81 Ca OD2 C:Asp87 4.70 Ca O C:Gly105 4.85 Ca CA C:Gly105 4.76 Ca CZ C:Phe107 4.36 Ca CE1 C:Phe107 4.94 Ca CB C:Asp124 4.26 Ca OD2 C:Asp124 2.40 Ca OD1 C:Asp124 2.51 Ca CG C:Asp124 2.78 Ca O C:Phe126 2.44 Ca N C:Phe126 4.56 Ca CB C:Phe126 4.60 Ca CD2 C:Phe126 4.73 Ca C C:Phe126 3.64 Ca CA C:Phe126 4.50 Ca N C:Arg127 4.57 Ca C C:Arg127 4.69 Ca CA C:Arg127 4.60 Ca N C:Asn128 3.89 Ca CB C:Asn128 4.12 Ca ND2 C:Asn128 4.62 Ca OD1 C:Asn128 2.39 Ca CG C:Asn128 3.52 Ca CA C:Asn128 4.64 Ca NE1 C:Trp130 4.46 Ca CB C:Asp131 4.40 Ca OD2 C:Asp131 2.34 Ca OD1 C:Asp131 3.85 Ca CG C:Asp131 3.32 Ca MN C:Mn3300 4.67 Ca O C:Hoh3402 3.82 Ca O C:Hoh3403 2.34 Ca O C:Hoh3404 2.37 interactive model: Calcium binding site 4 out of 4 in 2du0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 2du0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asp87, D: Gly105, D: Phe107, D: Asp124, D: Phe126, D: Arg127, D: Asn128, D: Trp130, D: Asp131, D: Mn4300, D: Hoh4402, D: Hoh4404, D: Hoh4442, conact list: Atom Atom Distance (A) Ca O D:Asp87 4.68 Ca OD2 D:Asp87 4.91 Ca O D:Gly105 4.70 Ca CA D:Gly105 4.66 Ca CZ D:Phe107 4.40 Ca CE1 D:Phe107 4.89 Ca CB D:Asp124 4.12 Ca OD2 D:Asp124 2.36 Ca OD1 D:Asp124 2.34 Ca CG D:Asp124 2.65 Ca CA D:Asp124 4.99 Ca O D:Phe126 2.31 Ca N D:Phe126 4.35 Ca CB D:Phe126 4.40 Ca CD2 D:Phe126 4.69 Ca C D:Phe126 3.51 Ca CA D:Phe126 4.31 Ca N D:Arg127 4.48 Ca C D:Arg127 4.70 Ca CA D:Arg127 4.55 Ca N D:Asn128 3.96 Ca CB D:Asn128 4.23 Ca ND2 D:Asn128 4.79 Ca OD1 D:Asn128 2.56 Ca CG D:Asn128 3.67 Ca CA D:Asn128 4.73 Ca NE1 D:Trp130 4.70 Ca CB D:Asp131 4.49 Ca OD2 D:Asp131 2.35 Ca OD1 D:Asp131 3.78 Ca CG D:Asp131 3.33 Ca MN D:Mn4300 4.34 Ca O D:Hoh4402 4.29 Ca O D:Hoh4404 2.34 Ca O D:Hoh4442 2.46 interactive model: