Calcium in the structure of Crystal Structure of Peanut Lectin Gal-Beta-1,3-Gal Complex (pdb 2dv9)

The binding sites of Calcium atom in the structure of Crystal Structure of Peanut Lectin Gal-Beta-1,3-Gal Complex (pdb code 2dv9). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 2dv9 structure was solved by S.K.NATCHIAR, O.SRINIVAS, N.MITRA, A.SUROLIA, N.JAYARAMAN, M.VIJAYAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-2.5 Space group P21212 a (A) 127.770 b (A) 124.910 c (A) 76.280 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 25.7 Calcium Binding Sites: Calcium binding site 1 out of 4 in 2dv9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 2dv9. 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: Asp83, A: Gly104, A: Asp123, A: Tyr125, A: Ser126, A: Asn127, A: Asp132, A: Mn238, A: Hoh337, A: Hoh338, A: Hoh438, conact list: Atom Atom Distance (A) Ca O A:Asp83 4.95 Ca OD1 A:Asp83 4.72 Ca O A:Gly104 4.81 Ca CA A:Gly104 4.28 Ca CB A:Asp123 4.43 Ca OD2 A:Asp123 2.66 Ca OD1 A:Asp123 2.60 Ca CG A:Asp123 2.96 Ca O A:Tyr125 2.58 Ca N A:Tyr125 4.57 Ca CB A:Tyr125 4.68 Ca CD1 A:Tyr125 4.57 Ca C A:Tyr125 3.68 Ca CA A:Tyr125 4.55 Ca N A:Ser126 4.55 Ca C A:Ser126 4.57 Ca CA A:Ser126 4.57 Ca N A:Asn127 3.73 Ca CB A:Asn127 3.77 Ca ND2 A:Asn127 4.58 Ca OD1 A:Asn127 2.61 Ca CG A:Asn127 3.44 Ca CA A:Asn127 4.39 Ca CB A:Asp132 4.70 Ca OD2 A:Asp132 2.69 Ca OD1 A:Asp132 4.10 Ca CG A:Asp132 3.63 Ca MN A:Mn238 4.31 Ca O A:Hoh337 2.72 Ca O A:Hoh338 2.83 Ca O A:Hoh438 4.39 interactive model: Calcium binding site 2 out of 4 in 2dv9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 2dv9. 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: Asp83, B: Gly104, B: Asp123, B: Tyr125, B: Ser126, B: Asn127, B: Asp132, B: Mn238, B: Hoh1392, B: Hoh1393, B: Hoh1494, conact list: Atom Atom Distance (A) Ca O B:Asp83 4.94 Ca OD1 B:Asp83 4.90 Ca O B:Gly104 4.65 Ca CA B:Gly104 4.41 Ca CB B:Asp123 4.51 Ca OD2 B:Asp123 2.66 Ca OD1 B:Asp123 2.70 Ca CG B:Asp123 3.03 Ca O B:Tyr125 2.62 Ca N B:Tyr125 4.57 Ca CB B:Tyr125 4.56 Ca CD1 B:Tyr125 4.71 Ca C B:Tyr125 3.73 Ca CA B:Tyr125 4.50 Ca N B:Ser126 4.67 Ca C B:Ser126 4.80 Ca CA B:Ser126 4.77 Ca N B:Asn127 3.98 Ca CB B:Asn127 4.02 Ca ND2 B:Asn127 4.78 Ca OD1 B:Asn127 2.70 Ca CG B:Asn127 3.64 Ca CA B:Asn127 4.64 Ca CB B:Asp132 4.82 Ca OD2 B:Asp132 2.62 Ca OD1 B:Asp132 4.33 Ca CG B:Asp132 3.74 Ca MN B:Mn238 4.14 Ca O B:Hoh1392 2.70 Ca O B:Hoh1393 4.34 Ca O B:Hoh1494 2.73 interactive model: Calcium binding site 3 out of 4 in 2dv9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 2dv9. 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: Gly104, C: Asp123, C: Tyr125, C: Ser126, C: Asn127, C: Asp132, C: His137, C: Mn238, C: Hoh2332, C: Hoh2396, C: Hoh2397, conact list: Atom Atom Distance (A) Ca O C:Gly104 4.92 Ca CA C:Gly104 4.86 Ca CB C:Asp123 4.51 Ca OD2 C:Asp123 2.85 Ca OD1 C:Asp123 2.81 Ca CG C:Asp123 3.12 Ca O C:Tyr125 2.52 Ca N C:Tyr125 4.80 Ca CD1 C:Tyr125 4.87 Ca C C:Tyr125 3.72 Ca CA C:Tyr125 4.74 Ca N C:Ser126 4.50 Ca C C:Ser126 4.43 Ca CA C:Ser126 4.37 Ca N C:Asn127 3.61 Ca CB C:Asn127 3.81 Ca ND2 C:Asn127 4.64 Ca OD1 C:Asn127 2.75 Ca CG C:Asn127 3.53 Ca CA C:Asn127 4.34 Ca CB C:Asp132 4.37 Ca OD2 C:Asp132 2.53 Ca OD1 C:Asp132 3.69 Ca CG C:Asp132 3.30 Ca CE1 C:His137 4.83 Ca MN C:Mn238 3.92 Ca O C:Hoh2332 2.57 Ca O C:Hoh2396 3.92 Ca O C:Hoh2397 2.99 interactive model: Calcium binding site 4 out of 4 in 2dv9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 2dv9. 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: Asp83, D: Gly104, D: Asp123, D: Tyr125, D: Ser126, D: Asn127, D: Asp132, D: Mn238, D: Hoh352, D: Hoh353, D: Hoh354, conact list: Atom Atom Distance (A) Ca O D:Asp83 4.94 Ca OD1 D:Asp83 4.66 Ca O D:Gly104 4.71 Ca CA D:Gly104 4.35 Ca CB D:Asp123 4.55 Ca OD2 D:Asp123 2.68 Ca OD1 D:Asp123 2.72 Ca CG D:Asp123 3.05 Ca O D:Tyr125 2.53 Ca N D:Tyr125 4.47 Ca CB D:Tyr125 4.54 Ca CD1 D:Tyr125 4.62 Ca C D:Tyr125 3.61 Ca CA D:Tyr125 4.45 Ca N D:Ser126 4.49 Ca C D:Ser126 4.59 Ca CA D:Ser126 4.55 Ca N D:Asn127 3.72 Ca CB D:Asn127 3.87 Ca ND2 D:Asn127 4.70 Ca OD1 D:Asn127 2.75 Ca CG D:Asn127 3.57 Ca CA D:Asn127 4.43 Ca CB D:Asp132 4.69 Ca OD2 D:Asp132 2.67 Ca OD1 D:Asp132 4.10 Ca CG D:Asp132 3.62 Ca MN D:Mn238 4.32 Ca O D:Hoh352 2.69 Ca O D:Hoh353 2.75 Ca O D:Hoh354 4.57 interactive model: