Calcium in the structure of Crystal Structure of BC2L-A Lectin From Burkolderia Cenocepacia in Complex With Methyl-Heptoside (pdb 4aoc)

The binding sites of Calcium atom in the structure of Crystal Structure of BC2L-A Lectin From Burkolderia Cenocepacia in Complex With Methyl-Heptoside (pdb code 4aoc). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 4aoc structure was solved by R.MARCHETTI, L.MALINOVSKA, E.LAMEIGNERE, C.DECASTRO, G.CIOCI, P.KOSMA, M.WIMMEROVA, A.MOLINARO, A.IMBERTY, A.SILIPO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 93.1-2.7 Space group C2221 a (A) 50.000 b (A) 185.140 c (A) 186.210 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.228 Rfree (%) 25.32 Calcium Binding Sites: Calcium binding site 1 out of 10 in 4aoc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 4aoc. 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: Asn28, A: Ala29, A: Asp113, A: Asp115, A: Asn117, A: Asp118, B: Gly128, A: Ca1130, A: A1q1131, conact list: Atom Atom Distance (A) Ca O A:Asn28 2.42 Ca CB A:Asn28 3.90 Ca C A:Asn28 3.58 Ca CA A:Asn28 4.40 Ca N A:Ala29 4.52 Ca CB A:Ala29 4.95 Ca CA A:Ala29 4.65 Ca OD2 A:Asp113 4.80 Ca OD1 A:Asp113 4.80 Ca CB A:Asp115 4.38 Ca OD2 A:Asp115 2.15 Ca OD1 A:Asp115 3.13 Ca CG A:Asp115 2.97 Ca O A:Asn117 4.62 Ca N A:Asn117 4.76 Ca CB A:Asn117 4.63 Ca ND2 A:Asn117 3.82 Ca C A:Asn117 4.34 Ca OD1 A:Asn117 2.23 Ca CG A:Asn117 3.33 Ca CA A:Asn117 4.81 Ca N A:Asp118 4.23 Ca CB A:Asp118 4.43 Ca OD2 A:Asp118 4.50 Ca OD1 A:Asp118 2.36 Ca CG A:Asp118 3.60 Ca CA A:Asp118 4.15 Ca O B:Gly128 2.34 Ca C B:Gly128 3.40 Ca CA B:Gly128 4.72 Ca OXT B:Gly128 3.71 Ca CA A:Ca1130 3.84 Ca O5 A:A1q1131 4.90 Ca C1 A:A1q1131 4.70 Ca O3 A:A1q1131 2.47 Ca C2 A:A1q1131 3.41 Ca O2 A:A1q1131 2.51 Ca C4 A:A1q1131 3.78 Ca C3 A:A1q1131 3.31 Ca O4 A:A1q1131 4.48 interactive model: Calcium binding site 2 out of 10 in 4aoc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 4aoc. 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: Glu109, A: Asp110, A: Gly111, A: His112, A: Asp113, A: Ser114, A: Asp115, A: Tyr116, A: Asn117, A: Asp118, A: Ca1129, A: A1q1131, conact list: Atom Atom Distance (A) Ca OE1 A:Glu109 2.09 Ca CB A:Glu109 4.68 Ca OE2 A:Glu109 2.48 Ca CD A:Glu109 2.59 Ca CG A:Glu109 4.07 Ca CA A:Glu109 4.60 Ca N A:Asp110 4.50 Ca OD2 A:Asp110 4.95 Ca OD1 A:Asp110 3.85 Ca CG A:Asp110 4.60 Ca N A:Gly111 4.99 Ca N A:His112 4.97 Ca O A:Asp113 4.88 Ca N A:Asp113 4.22 Ca CB A:Asp113 4.53 Ca OD2 A:Asp113 3.84 Ca C A:Asp113 4.56 Ca OD1 A:Asp113 2.16 Ca CG A:Asp113 3.30 Ca CA A:Asp113 4.62 Ca N A:Ser114 4.74 Ca N A:Asp115 4.20 Ca CB A:Asp115 4.69 Ca OD2 A:Asp115 3.92 Ca OD1 A:Asp115 2.39 Ca CG A:Asp115 3.46 Ca CA A:Asp115 4.84 Ca N A:Tyr116 4.43 Ca OD1 A:Asn117 4.86 Ca CB A:Asp118 4.35 Ca OD2 A:Asp118 2.39 Ca OD1 A:Asp118 2.54 Ca CG A:Asp118 2.81 Ca CA A:Ca1129 3.84 Ca O3 A:A1q1131 2.50 Ca C2 A:A1q1131 4.67 Ca C5 A:A1q1131 4.57 Ca O2 A:A1q1131 4.92 Ca C4 A:A1q1131 3.14 Ca C3 A:A1q1131 3.27 Ca O4 A:A1q1131 2.34 interactive model: Calcium binding site 3 out of 10 in 4aoc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 4aoc. 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: Gly128, B: Asn28, B: Ala29, B: Asp113, B: Asp115, B: Asn117, B: Asp118, B: Ca1130, B: A1q1131, conact list: Atom Atom Distance (A) Ca O A:Gly128 2.26 Ca C A:Gly128 3.26 Ca CA A:Gly128 4.58 Ca OXT A:Gly128 3.52 Ca O B:Asn28 2.35 Ca CB B:Asn28 4.06 Ca C B:Asn28 3.51 Ca CA B:Asn28 4.45 Ca N B:Ala29 4.38 Ca CB B:Ala29 4.95 Ca CA B:Ala29 4.49 Ca OD2 B:Asp113 4.48 Ca OD1 B:Asp113 4.94 Ca CB B:Asp115 4.53 Ca OD2 B:Asp115 2.39 Ca OD1 B:Asp115 2.97 Ca CG B:Asp115 3.05 Ca O B:Asn117 4.63 Ca N B:Asn117 4.82 Ca CB B:Asn117 4.67 Ca ND2 B:Asn117 3.79 Ca C B:Asn117 4.40 Ca OD1 B:Asn117 2.28 Ca CG B:Asn117 3.35 Ca CA B:Asn117 4.90 Ca N B:Asp118 4.32 Ca CB B:Asp118 4.54 Ca OD2 B:Asp118 4.60 Ca OD1 B:Asp118 2.48 Ca CG B:Asp118 3.72 Ca CA B:Asp118 4.20 Ca CA B:Ca1130 3.68 Ca C1 B:A1q1131 4.76 Ca O3 B:A1q1131 2.53 Ca C2 B:A1q1131 3.48 Ca O2 B:A1q1131 2.50 Ca C4 B:A1q1131 3.74 Ca C3 B:A1q1131 3.36 Ca O4 B:A1q1131 4.30 interactive model: Calcium binding site 4 out of 10 in 4aoc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 4aoc. 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: Glu109, B: Asp110, B: Asp113, B: Ser114, B: Asp115, B: Tyr116, B: Asn117, B: Asp118, B: Ca1129, B: A1q1131, conact list: Atom Atom Distance (A) Ca OE1 B:Glu109 2.25 Ca CB B:Glu109 4.97 Ca OE2 B:Glu109 2.60 Ca CD B:Glu109 2.77 Ca CG B:Glu109 4.29 Ca CA B:Glu109 4.77 Ca N B:Asp110 4.60 Ca OD1 B:Asp110 3.93 Ca CG B:Asp110 4.72 Ca O B:Asp113 4.59 Ca N B:Asp113 4.30 Ca CB B:Asp113 4.43 Ca OD2 B:Asp113 3.37 Ca C B:Asp113 4.44 Ca OD1 B:Asp113 2.36 Ca CG B:Asp113 3.14 Ca CA B:Asp113 4.63 Ca N B:Ser114 4.73 Ca N B:Asp115 4.26 Ca CB B:Asp115 4.68 Ca OD2 B:Asp115 4.00 Ca OD1 B:Asp115 2.49 Ca CG B:Asp115 3.50 Ca CA B:Asp115 4.82 Ca N B:Tyr116 4.40 Ca OD1 B:Asn117 4.69 Ca CB B:Asp118 4.34 Ca OD2 B:Asp118 2.50 Ca OD1 B:Asp118 2.51 Ca CG B:Asp118 2.84 Ca CA B:Ca1129 3.68 Ca O3 B:A1q1131 2.38 Ca C2 B:A1q1131 4.66 Ca C5 B:A1q1131 4.67 Ca O2 B:A1q1131 4.80 Ca C4 B:A1q1131 3.27 Ca C3 B:A1q1131 3.28 Ca O4 B:A1q1131 2.46 interactive model: Calcium binding site 5 out of 10 in 4aoc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 4aoc. 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: Asn28, C: Ala29, C: Asp113, C: Asp115, C: Asn117, C: Asp118, E: Gly128, C: Ca1130, C: A1q1131, conact list: Atom Atom Distance (A) Ca O C:Asn28 2.33 Ca CB C:Asn28 4.09 Ca C C:Asn28 3.55 Ca CA C:Asn28 4.47 Ca N C:Ala29 4.48 Ca CA C:Ala29 4.56 Ca OD2 C:Asp113 4.51 Ca OD1 C:Asp113 4.74 Ca CB C:Asp115 4.47 Ca OD2 C:Asp115 2.26 Ca OD1 C:Asp115 3.08 Ca CG C:Asp115 3.02 Ca O C:Asn117 4.63 Ca N C:Asn117 4.79 Ca CB C:Asn117 4.74 Ca ND2 C:Asn117 3.98 Ca C C:Asn117 4.34 Ca OD1 C:Asn117 2.35 Ca CG C:Asn117 3.47 Ca CA C:Asn117 4.87 Ca N C:Asp118 4.16 Ca CB C:Asp118 4.39 Ca OD2 C:Asp118 4.48 Ca OD1 C:Asp118 2.34 Ca CG C:Asp118 3.59 Ca CA C:Asp118 4.08 Ca O E:Gly128 3.96 Ca C E:Gly128 3.52 Ca CA E:Gly128 4.75 Ca OXT E:Gly128 2.39 Ca CA C:Ca1130 3.60 Ca O5 C:A1q1131 4.99 Ca C1 C:A1q1131 4.81 Ca O3 C:A1q1131 2.31 Ca C2 C:A1q1131 3.51 Ca C5 C:A1q1131 4.98 Ca O2 C:A1q1131 2.67 Ca C4 C:A1q1131 3.67 Ca C3 C:A1q1131 3.27 Ca O4 C:A1q1131 4.25 interactive model: Calcium binding site 6 out of 10 in 4aoc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Calcium in the PDB 4aoc. 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: Glu109, C: Asp110, C: His112, C: Asp113, C: Ser114, C: Asp115, C: Tyr116, C: Asn117, C: Asp118, C: Ca1129, C: A1q1131, conact list: Atom Atom Distance (A) Ca OE1 C:Glu109 2.44 Ca CB C:Glu109 4.98 Ca OE2 C:Glu109 2.52 Ca CD C:Glu109 2.82 Ca CG C:Glu109 4.33 Ca CA C:Glu109 4.73 Ca N C:Asp110 4.47 Ca OD1 C:Asp110 3.93 Ca CG C:Asp110 4.64 Ca N C:His112 4.91 Ca CB C:His112 4.93 Ca O C:Asp113 4.61 Ca N C:Asp113 4.14 Ca CB C:Asp113 4.48 Ca OD2 C:Asp113 3.63 Ca C C:Asp113 4.47 Ca OD1 C:Asp113 2.20 Ca CG C:Asp113 3.22 Ca CA C:Asp113 4.61 Ca N C:Ser114 4.79 Ca N C:Asp115 4.33 Ca CB C:Asp115 4.68 Ca OD2 C:Asp115 3.80 Ca OD1 C:Asp115 2.35 Ca CG C:Asp115 3.39 Ca CA C:Asp115 4.90 Ca N C:Tyr116 4.57 Ca OD1 C:Asn117 4.90 Ca CB C:Asp118 4.33 Ca OD2 C:Asp118 2.46 Ca OD1 C:Asp118 2.48 Ca CG C:Asp118 2.81 Ca CA C:Ca1129 3.60 Ca O3 C:A1q1131 2.64 Ca C2 C:A1q1131 4.79 Ca C5 C:A1q1131 4.68 Ca O2 C:A1q1131 4.99 Ca C4 C:A1q1131 3.30 Ca C3 C:A1q1131 3.40 Ca O4 C:A1q1131 2.48 interactive model: Calcium binding site 7 out of 10 in 4aoc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Calcium in the PDB 4aoc. 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: Asn28, D: Ala29, D: Asp113, D: Asp115, D: Asn117, D: Asp118, D: Ca1130, D: A1q1131, conact list: Atom Atom Distance (A) Ca O D:Asn28 2.39 Ca CB D:Asn28 4.11 Ca C D:Asn28 3.57 Ca CA D:Asn28 4.50 Ca N D:Ala29 4.44 Ca CB D:Ala29 4.87 Ca CA D:Ala29 4.52 Ca OD2 D:Asp113 4.56 Ca OD1 D:Asp113 4.78 Ca CB D:Asp115 4.38 Ca OD2 D:Asp115 2.22 Ca OD1 D:Asp115 3.06 Ca CG D:Asp115 2.97 Ca O D:Asn117 4.73 Ca N D:Asn117 4.75 Ca CB D:Asn117 4.60 Ca ND2 D:Asn117 3.75 Ca C D:Asn117 4.45 Ca OD1 D:Asn117 2.20 Ca CG D:Asn117 3.28 Ca CA D:Asn117 4.84 Ca N D:Asp118 4.43 Ca CB D:Asp118 4.49 Ca OD2 D:Asp118 4.37 Ca OD1 D:Asp118 2.33 Ca CG D:Asp118 3.57 Ca CA D:Asp118 4.31 Ca CA D:Ca1130 3.84 Ca C1 D:A1q1131 4.80 Ca O3 D:A1q1131 2.53 Ca C2 D:A1q1131 3.49 Ca O2 D:A1q1131 2.52 Ca C4 D:A1q1131 3.93 Ca C3 D:A1q1131 3.44 Ca O4 D:A1q1131 4.56 interactive model: Calcium binding site 8 out of 10 in 4aoc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Calcium in the PDB 4aoc. 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: Glu109, D: Asp110, D: Gly111, D: Asp113, D: Ser114, D: Asp115, D: Tyr116, D: Asn117, D: Asp118, D: Ca1129, D: A1q1131, conact list: Atom Atom Distance (A) Ca OE1 D:Glu109 2.44 Ca CB D:Glu109 4.87 Ca OE2 D:Glu109 2.50 Ca CD D:Glu109 2.78 Ca C D:Glu109 4.92 Ca CG D:Glu109 4.27 Ca CA D:Glu109 4.58 Ca N D:Asp110 4.30 Ca OD2 D:Asp110 4.89 Ca OD1 D:Asp110 3.91 Ca CG D:Asp110 4.55 Ca N D:Gly111 4.93 Ca O D:Asp113 4.58 Ca N D:Asp113 4.27 Ca CB D:Asp113 4.51 Ca OD2 D:Asp113 3.70 Ca C D:Asp113 4.48 Ca OD1 D:Asp113 2.20 Ca CG D:Asp113 3.25 Ca CA D:Asp113 4.65 Ca N D:Ser114 4.80 Ca N D:Asp115 4.18 Ca CB D:Asp115 4.67 Ca OD2 D:Asp115 3.95 Ca OD1 D:Asp115 2.48 Ca CG D:Asp115 3.48 Ca CA D:Asp115 4.78 Ca N D:Tyr116 4.36 Ca OD1 D:Asn117 4.75 Ca CB D:Asp118 4.30 Ca OD2 D:Asp118 2.22 Ca OD1 D:Asp118 2.73 Ca CG D:Asp118 2.82 Ca CA D:Ca1129 3.84 Ca O3 D:A1q1131 2.57 Ca C2 D:A1q1131 4.82 Ca C5 D:A1q1131 4.82 Ca O2 D:A1q1131 4.94 Ca C4 D:A1q1131 3.38 Ca C3 D:A1q1131 3.47 Ca O4 D:A1q1131 2.58 interactive model: Calcium binding site 9 out of 10 in 4aoc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Calcium in the PDB 4aoc. 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: Gly128, E: Asn28, E: Ala29, E: Asp113, E: Asp115, E: Asn117, E: Asp118, E: Ca1130, E: A1q1131, conact list: Atom Atom Distance (A) Ca O C:Gly128 2.51 Ca C C:Gly128 3.51 Ca CA C:Gly128 4.89 Ca OXT C:Gly128 3.74 Ca O E:Asn28 2.18 Ca CB E:Asn28 3.96 Ca C E:Asn28 3.41 Ca CA E:Asn28 4.35 Ca N E:Ala29 4.32 Ca CB E:Ala29 4.62 Ca CA E:Ala29 4.36 Ca OD2 E:Asp113 4.80 Ca OD1 E:Asp113 4.81 Ca CB E:Asp115 4.44 Ca OD2 E:Asp115 2.28 Ca OD1 E:Asp115 3.18 Ca CG E:Asp115 3.06 Ca O E:Asn117 4.56 Ca N E:Asn117 4.82 Ca CB E:Asn117 4.68 Ca ND2 E:Asn117 3.86 Ca C E:Asn117 4.32 Ca OD1 E:Asn117 2.30 Ca CG E:Asn117 3.39 Ca CA E:Asn117 4.84 Ca N E:Asp118 4.22 Ca CB E:Asp118 4.48 Ca OD2 E:Asp118 4.45 Ca OD1 E:Asp118 2.36 Ca CG E:Asp118 3.61 Ca CA E:Asp118 4.17 Ca CA E:Ca1130 3.68 Ca C1 E:A1q1131 4.84 Ca O3 E:A1q1131 2.38 Ca C2 E:A1q1131 3.51 Ca O2 E:A1q1131 2.66 Ca C4 E:A1q1131 3.80 Ca C3 E:A1q1131 3.32 Ca O4 E:A1q1131 4.42 interactive model: Calcium binding site 10 out of 10 in 4aoc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Calcium in the PDB 4aoc. 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: E: Glu109, E: Asp110, E: Gly111, E: His112, E: Asp113, E: Ser114, E: Asp115, E: Tyr116, E: Asn117, E: Asp118, E: Ca1129, E: A1q1131, conact list: Atom Atom Distance (A) Ca OE1 E:Glu109 2.46 Ca OE2 E:Glu109 2.50 Ca CD E:Glu109 2.82 Ca CG E:Glu109 4.33 Ca CA E:Glu109 4.88 Ca N E:Asp110 4.75 Ca OD2 E:Asp110 4.81 Ca OD1 E:Asp110 3.79 Ca CG E:Asp110 4.56 Ca N E:Gly111 4.98 Ca N E:His112 4.88 Ca C E:His112 4.99 Ca O E:Asp113 4.35 Ca N E:Asp113 4.08 Ca CB E:Asp113 4.45 Ca OD2 E:Asp113 3.63 Ca C E:Asp113 4.40 Ca OD1 E:Asp113 2.24 Ca CG E:Asp113 3.21 Ca CA E:Asp113 4.55 Ca N E:Ser114 4.89 Ca N E:Asp115 4.38 Ca CB E:Asp115 4.70 Ca OD2 E:Asp115 3.78 Ca OD1 E:Asp115 2.37 Ca CG E:Asp115 3.40 Ca CA E:Asp115 4.95 Ca N E:Tyr116 4.62 Ca OD1 E:Asn117 4.85 Ca CB E:Asp118 4.36 Ca OD2 E:Asp118 2.37 Ca OD1 E:Asp118 2.59 Ca CG E:Asp118 2.83 Ca CA E:Ca1129 3.68 Ca O3 E:A1q1131 2.43 Ca C2 E:A1q1131 4.67 Ca C5 E:A1q1131 4.58 Ca O2 E:A1q1131 4.90 Ca C4 E:A1q1131 3.18 Ca C3 E:A1q1131 3.25 Ca O4 E:A1q1131 2.41 interactive model: