Calcium in the structure of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form At Acidic pH (pdb 1v6j)

The binding sites of Calcium atom in the structure of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form At Acidic pH (pdb code 1v6j). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 1v6j structure was solved by S.KUNDHAVAI NATCHIAR, A.AROCKIA JEYAPRAKASH, T.N.C.RAMYA, C.J.THOMAS, K.SUGUNA, A.SUROLIA, M.VIJAYAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.9 Space group P21212 a (A) 128.733 b (A) 125.531 c (A) 76.050 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.1 Rfree (%) 22 Calcium Binding Sites: Calcium binding site 1 out of 4 in 1v6j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 1v6j. 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, conact list: Atom Atom Distance (A) Ca O A:Asp83 4.46 Ca OD1 A:Asp83 4.46 Ca O A:Gly104 4.30 Ca C A:Gly104 4.65 Ca CA A:Gly104 3.98 Ca CB A:Asp123 4.61 Ca OD2 A:Asp123 2.85 Ca OD1 A:Asp123 2.66 Ca CG A:Asp123 3.11 Ca O A:Tyr125 2.68 Ca N A:Tyr125 4.69 Ca CB A:Tyr125 4.75 Ca CD1 A:Tyr125 4.80 Ca C A:Tyr125 3.86 Ca CA A:Tyr125 4.67 Ca N A:Ser126 4.82 Ca C A:Ser126 4.87 Ca CA A:Ser126 4.91 Ca N A:Asn127 4.05 Ca CB A:Asn127 3.82 Ca ND2 A:Asn127 4.63 Ca OD1 A:Asn127 2.81 Ca CG A:Asn127 3.54 Ca CA A:Asn127 4.59 Ca OD2 A:Asp132 2.68 Ca OD1 A:Asp132 4.32 Ca CG A:Asp132 3.82 Ca MN A:Mn238 4.79 interactive model: Calcium binding site 2 out of 4 in 1v6j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 1v6j. 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, conact list: Atom Atom Distance (A) Ca O B:Asp83 4.41 Ca CB B:Asp83 4.42 Ca O B:Gly104 4.29 Ca C B:Gly104 4.65 Ca CA B:Gly104 3.97 Ca CB B:Asp123 4.56 Ca OD2 B:Asp123 2.75 Ca OD1 B:Asp123 2.65 Ca CG B:Asp123 3.06 Ca O B:Tyr125 2.72 Ca N B:Tyr125 4.74 Ca CB B:Tyr125 4.70 Ca CD1 B:Tyr125 4.75 Ca C B:Tyr125 3.85 Ca CA B:Tyr125 4.66 Ca N B:Ser126 4.77 Ca C B:Ser126 4.88 Ca CA B:Ser126 4.88 Ca N B:Asn127 4.27 Ca CB B:Asn127 4.12 Ca ND2 B:Asn127 4.43 Ca OD1 B:Asn127 2.63 Ca CG B:Asn127 3.50 Ca CA B:Asn127 4.86 Ca OD2 B:Asp132 2.73 Ca OD1 B:Asp132 4.33 Ca CG B:Asp132 3.85 Ca MN B:Mn238 4.70 interactive model: Calcium binding site 3 out of 4 in 1v6j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 1v6j. 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: Asp83, C: Gly104, C: Asp123, C: Tyr125, C: Ser126, C: Asn127, C: Asp132, C: Mn238, conact list: Atom Atom Distance (A) Ca O C:Asp83 4.65 Ca CB C:Asp83 4.67 Ca OD1 C:Asp83 4.70 Ca O C:Gly104 4.45 Ca C C:Gly104 4.90 Ca CA C:Gly104 4.32 Ca CB C:Asp123 4.60 Ca OD2 C:Asp123 2.81 Ca OD1 C:Asp123 2.71 Ca CG C:Asp123 3.11 Ca O C:Tyr125 2.70 Ca N C:Tyr125 4.66 Ca CB C:Tyr125 4.53 Ca CD1 C:Tyr125 4.62 Ca C C:Tyr125 3.78 Ca CA C:Tyr125 4.56 Ca N C:Ser126 4.68 Ca C C:Ser126 4.75 Ca CA C:Ser126 4.77 Ca N C:Asn127 3.91 Ca CB C:Asn127 3.83 Ca ND2 C:Asn127 4.55 Ca OD1 C:Asn127 2.77 Ca CG C:Asn127 3.50 Ca CA C:Asn127 4.51 Ca CB C:Asp132 4.96 Ca OD2 C:Asp132 2.74 Ca OD1 C:Asp132 4.36 Ca CG C:Asp132 3.84 Ca MN C:Mn238 4.75 interactive model: Calcium binding site 4 out of 4 in 1v6j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 1v6j. 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, conact list: Atom Atom Distance (A) Ca O D:Asp83 4.62 Ca CB D:Asp83 4.43 Ca OD1 D:Asp83 4.62 Ca O D:Gly104 4.32 Ca C D:Gly104 4.67 Ca CA D:Gly104 3.99 Ca CB D:Asp123 4.63 Ca OD2 D:Asp123 2.76 Ca OD1 D:Asp123 2.78 Ca CG D:Asp123 3.13 Ca O D:Tyr125 2.77 Ca N D:Tyr125 4.81 Ca CB D:Tyr125 4.74 Ca CD1 D:Tyr125 4.84 Ca C D:Tyr125 3.91 Ca CA D:Tyr125 4.72 Ca N D:Ser126 4.83 Ca C D:Ser126 4.77 Ca CA D:Ser126 4.91 Ca N D:Asn127 4.08 Ca CB D:Asn127 3.74 Ca ND2 D:Asn127 3.97 Ca OD1 D:Asn127 2.95 Ca CG D:Asn127 3.29 Ca CA D:Asn127 4.55 Ca OD2 D:Asp132 2.78 Ca OD1 D:Asp132 4.32 Ca CG D:Asp132 3.86 Ca MN D:Mn238 4.99 interactive model: