Calcium in the structure of Mannose-Binding Protein-A Mutant (Qpdwgh) Complexed With N- Acetyl-D-Galactosamine (pdb 1bch)

The binding sites of Calcium atom in the structure of Mannose-Binding Protein-A Mutant (Qpdwgh) Complexed With N- Acetyl-D-Galactosamine (pdb code 1bch). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 1bch structure was solved by A.R.KOLATKAR, W.I.WEIS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.0 Space group C121 a (A) 80.490 b (A) 85.010 c (A) 98.710 alpha (°) 90.00 beta (°) 104.82 gamma (°) 90.00 Rfactor (%) 21.9 Rfree (%) 25.2 Calcium Binding Sites: Calcium binding site 1 out of 9 in 1bch Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 1bch. 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: 1: Asp161, 1: Glu165, 1: Gly166, 1: Phe168, 1: Asp188, 1: Glu198, 1: Asp199, 1: Asp211, 1: Hoh241, 1: Hoh242, 1: Hoh274, 1: Hoh275, conact list: Atom Atom Distance (A) Ca O 1:Asp161 4.69 Ca CB 1:Asp161 4.44 Ca OD2 1:Asp161 2.45 Ca OD1 1:Asp161 2.71 Ca CG 1:Asp161 2.93 Ca OE1 1:Glu165 2.49 Ca OE2 1:Glu165 2.58 Ca CD 1:Glu165 2.86 Ca CG 1:Glu165 4.36 Ca CA 1:Glu165 4.88 Ca N 1:Gly166 4.64 Ca CZ 1:Phe168 4.61 Ca CB 1:Asp188 3.83 Ca OD2 1:Asp188 4.09 Ca OD1 1:Asp188 2.53 Ca CG 1:Asp188 3.27 Ca CA 1:Asp188 4.35 Ca O 1:Glu198 2.42 Ca N 1:Glu198 4.32 Ca C 1:Glu198 3.37 Ca CA 1:Glu198 4.48 Ca N 1:Asp199 3.94 Ca CB 1:Asp199 4.22 Ca OD2 1:Asp199 4.51 Ca C 1:Asp199 4.99 Ca OD1 1:Asp199 2.45 Ca CG 1:Asp199 3.56 Ca CA 1:Asp199 3.77 Ca OD2 1:Asp211 4.71 Ca O 1:Hoh241 2.39 Ca O 1:Hoh242 4.74 Ca O 1:Hoh274 4.03 Ca O 1:Hoh275 4.61 interactive model: Calcium binding site 2 out of 9 in 1bch Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 1bch. 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: 1: Gln185, 1: Asp187, 1: Asp188, 1: Trp189, 1: Glu198, 1: Asn210, 1: Asp211, 1: Ile212, 1: A2g1, conact list: Atom Atom Distance (A) Ca NE2 1:Gln185 3.83 Ca OE1 1:Gln185 2.56 Ca CD 1:Gln185 3.40 Ca CG 1:Gln185 4.55 Ca N 1:Asp187 4.25 Ca CB 1:Asp187 4.66 Ca OD2 1:Asp187 3.81 Ca OD1 1:Asp187 2.46 Ca CG 1:Asp187 3.43 Ca CA 1:Asp187 4.88 Ca N 1:Asp188 4.87 Ca N 1:Trp189 4.80 Ca CB 1:Trp189 4.56 Ca OE1 1:Glu198 2.40 Ca CB 1:Glu198 4.78 Ca OE2 1:Glu198 3.58 Ca CD 1:Glu198 3.29 Ca CG 1:Glu198 4.59 Ca CB 1:Asn210 4.78 Ca ND2 1:Asn210 3.75 Ca C 1:Asn210 4.64 Ca OD1 1:Asn210 2.54 Ca CG 1:Asn210 3.45 Ca CA 1:Asn210 4.99 Ca O 1:Asp211 2.53 Ca N 1:Asp211 3.78 Ca CB 1:Asp211 4.29 Ca OD2 1:Asp211 4.08 Ca C 1:Asp211 3.60 Ca OD1 1:Asp211 2.28 Ca CG 1:Asp211 3.33 Ca CA 1:Asp211 4.10 Ca N 1:Ile212 4.74 Ca O3 1:A2g1 2.46 Ca O3 1:A2g1 2.63 Ca C2 1:A2g1 4.21 Ca C2 1:A2g1 4.28 Ca C5 1:A2g1 4.76 Ca C5 1:A2g1 4.88 Ca C4 1:A2g1 3.30 Ca C4 1:A2g1 3.46 Ca C3 1:A2g1 3.40 Ca C3 1:A2g1 3.56 Ca O4 1:A2g1 2.58 Ca O4 1:A2g1 2.61 interactive model: Calcium binding site 3 out of 9 in 1bch Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 1bch. 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: 1: Asn80, 1: Glu84, 1: Hoh228, 2: Hoh234, conact list: Atom Atom Distance (A) Ca ND2 1:Asn80 4.56 Ca OD1 1:Asn80 4.50 Ca CG 1:Asn80 5.00 Ca OE1 1:Glu84 3.96 Ca OE2 1:Glu84 2.36 Ca CD 1:Glu84 3.48 Ca CG 1:Glu84 4.72 Ca O 1:Hoh228 2.47 Ca O 2:Hoh234 4.57 interactive model: Calcium binding site 4 out of 9 in 1bch Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 1bch. 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: 2: Asp161, 2: Glu165, 2: Gly166, 2: Phe168, 2: Asp188, 2: Glu198, 2: Asp199, 2: Asp211, 2: Ca3, 2: Hoh261, 2: Hoh272, 2: Hoh293, conact list: Atom Atom Distance (A) Ca O 2:Asp161 4.63 Ca CB 2:Asp161 4.44 Ca OD2 2:Asp161 2.48 Ca OD1 2:Asp161 2.68 Ca CG 2:Asp161 2.93 Ca OE1 2:Glu165 2.58 Ca OE2 2:Glu165 2.60 Ca CD 2:Glu165 2.92 Ca CG 2:Glu165 4.42 Ca CA 2:Glu165 4.93 Ca N 2:Gly166 4.80 Ca CZ 2:Phe168 4.54 Ca CB 2:Asp188 3.85 Ca OD2 2:Asp188 3.97 Ca OD1 2:Asp188 2.69 Ca CG 2:Asp188 3.27 Ca CA 2:Asp188 4.40 Ca O 2:Glu198 2.44 Ca N 2:Glu198 4.29 Ca C 2:Glu198 3.27 Ca CA 2:Glu198 4.38 Ca N 2:Asp199 3.78 Ca CB 2:Asp199 4.20 Ca OD2 2:Asp199 4.61 Ca C 2:Asp199 4.85 Ca OD1 2:Asp199 2.46 Ca CG 2:Asp199 3.61 Ca CA 2:Asp199 3.65 Ca OD2 2:Asp211 4.56 Ca CA 2:Ca3 3.98 Ca O 2:Hoh261 4.50 Ca O 2:Hoh272 2.25 Ca O 2:Hoh293 3.93 interactive model: Calcium binding site 5 out of 9 in 1bch Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 1bch. 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: 2: Gln185, 2: Asp187, 2: Asp188, 2: Trp189, 2: Glu198, 2: Asn210, 2: Asp211, 2: Ile212, 2: Nga1, conact list: Atom Atom Distance (A) Ca NE2 2:Gln185 3.84 Ca OE1 2:Gln185 2.40 Ca CD 2:Gln185 3.35 Ca CG 2:Gln185 4.51 Ca N 2:Asp187 4.29 Ca CB 2:Asp187 4.71 Ca OD2 2:Asp187 3.92 Ca OD1 2:Asp187 2.41 Ca CG 2:Asp187 3.48 Ca CA 2:Asp187 4.94 Ca N 2:Asp188 4.76 Ca N 2:Trp189 4.71 Ca CB 2:Trp189 4.52 Ca OE1 2:Glu198 2.23 Ca CB 2:Glu198 4.71 Ca OE2 2:Glu198 3.71 Ca CD 2:Glu198 3.29 Ca CG 2:Glu198 4.57 Ca CB 2:Asn210 4.79 Ca ND2 2:Asn210 3.92 Ca C 2:Asn210 4.59 Ca OD1 2:Asn210 2.52 Ca CG 2:Asn210 3.51 Ca CA 2:Asn210 4.96 Ca O 2:Asp211 2.47 Ca N 2:Asp211 3.74 Ca CB 2:Asp211 4.28 Ca OD2 2:Asp211 4.12 Ca C 2:Asp211 3.54 Ca OD1 2:Asp211 2.36 Ca CG 2:Asp211 3.37 Ca CA 2:Asp211 4.05 Ca N 2:Ile212 4.68 Ca O3 2:Nga1 2.57 Ca C2 2:Nga1 4.22 Ca C5 2:Nga1 4.88 Ca C4 2:Nga1 3.46 Ca C3 2:Nga1 3.51 Ca O4 2:Nga1 2.66 interactive model: Calcium binding site 6 out of 9 in 1bch Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Calcium in the PDB 1bch. 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: 2: Asp161, 2: Glu162, 2: Glu165, 2: Asp188, 2: Asp199, 2: Ca227, 2: Hoh271, 2: Hoh293, 2: Hoh310, 2: Hoh311, 2: Hoh312, conact list: Atom Atom Distance (A) Ca O 2:Asp161 4.17 Ca OD2 2:Asp161 4.82 Ca OD1 2:Asp161 4.96 Ca O 2:Glu162 4.83 Ca N 2:Glu165 4.92 Ca OE1 2:Glu165 2.26 Ca CB 2:Glu165 3.92 Ca OE2 2:Glu165 4.45 Ca CD 2:Glu165 3.44 Ca CG 2:Glu165 4.07 Ca CA 2:Glu165 4.42 Ca OD2 2:Asp188 4.62 Ca OD1 2:Asp188 4.34 Ca CG 2:Asp188 4.87 Ca CB 2:Asp199 4.29 Ca OD2 2:Asp199 2.46 Ca OD1 2:Asp199 2.44 Ca CG 2:Asp199 2.78 Ca CA 2:Ca227 3.98 Ca O 2:Hoh271 4.71 Ca O 2:Hoh293 2.26 Ca O 2:Hoh310 2.51 Ca O 2:Hoh311 2.61 Ca O 2:Hoh312 2.38 interactive model: Calcium binding site 7 out of 9 in 1bch Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Calcium in the PDB 1bch. 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: 3: Asp161, 3: Glu165, 3: Gly166, 3: Phe168, 3: Asp188, 3: Glu198, 3: Asp199, 3: Asp211, 3: Hoh242, 3: Hoh244, 3: Hoh276, conact list: Atom Atom Distance (A) Ca O 3:Asp161 4.75 Ca CB 3:Asp161 4.53 Ca OD2 3:Asp161 2.52 Ca OD1 3:Asp161 2.80 Ca CG 3:Asp161 3.02 Ca OE1 3:Glu165 2.49 Ca OE2 3:Glu165 2.69 Ca CD 3:Glu165 2.93 Ca CG 3:Glu165 4.44 Ca CA 3:Glu165 4.93 Ca N 3:Gly166 4.65 Ca CZ 3:Phe168 4.67 Ca CB 3:Asp188 3.74 Ca OD2 3:Asp188 4.18 Ca OD1 3:Asp188 2.55 Ca CG 3:Asp188 3.29 Ca CA 3:Asp188 4.36 Ca O 3:Glu198 2.35 Ca N 3:Glu198 4.27 Ca C 3:Glu198 3.25 Ca CA 3:Glu198 4.34 Ca N 3:Asp199 3.82 Ca CB 3:Asp199 4.15 Ca OD2 3:Asp199 4.41 Ca C 3:Asp199 4.95 Ca OD1 3:Asp199 2.43 Ca CG 3:Asp199 3.49 Ca CA 3:Asp199 3.69 Ca OD2 3:Asp211 4.83 Ca O 3:Hoh242 2.40 Ca O 3:Hoh244 4.82 Ca O 3:Hoh276 4.69 interactive model: Calcium binding site 8 out of 9 in 1bch Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Calcium in the PDB 1bch. 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: 3: Gln185, 3: Asp187, 3: Asp188, 3: Trp189, 3: Glu198, 3: Asn210, 3: Asp211, 3: Ile212, 3: Nga1, conact list: Atom Atom Distance (A) Ca NE2 3:Gln185 3.64 Ca OE1 3:Gln185 2.39 Ca CD 3:Gln185 3.25 Ca CG 3:Gln185 4.47 Ca N 3:Asp187 4.30 Ca CB 3:Asp187 4.74 Ca OD2 3:Asp187 3.86 Ca OD1 3:Asp187 2.51 Ca CG 3:Asp187 3.50 Ca CA 3:Asp187 4.97 Ca N 3:Asp188 4.92 Ca N 3:Trp189 4.89 Ca CB 3:Trp189 4.66 Ca OE1 3:Glu198 2.42 Ca CB 3:Glu198 4.83 Ca OE2 3:Glu198 3.76 Ca CD 3:Glu198 3.39 Ca CG 3:Glu198 4.67 Ca CB 3:Asn210 4.83 Ca ND2 3:Asn210 3.82 Ca C 3:Asn210 4.69 Ca OD1 3:Asn210 2.57 Ca CG 3:Asn210 3.50 Ca O 3:Asp211 2.53 Ca N 3:Asp211 3.81 Ca CB 3:Asp211 4.29 Ca OD2 3:Asp211 3.99 Ca C 3:Asp211 3.61 Ca OD1 3:Asp211 2.11 Ca CG 3:Asp211 3.26 Ca CA 3:Asp211 4.13 Ca N 3:Ile212 4.75 Ca O3 3:Nga1 2.47 Ca C2 3:Nga1 4.22 Ca C5 3:Nga1 4.80 Ca C4 3:Nga1 3.37 Ca C3 3:Nga1 3.43 Ca O4 3:Nga1 2.60 interactive model: Calcium binding site 9 out of 9 in 1bch Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Calcium in the PDB 1bch. 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: 1: Lys89, 3: Asn80, 3: Glu84, 1: Hoh239, 1: Hoh271, 3: Hoh228, 3: Hoh236, 3: Hoh248, 3: Hoh249, 3: Hoh290, 3: Hoh296, conact list: Atom Atom Distance (A) Ca NZ 1:Lys89 4.21 Ca ND2 3:Asn80 4.60 Ca OD1 3:Asn80 4.62 Ca OE1 3:Glu84 3.98 Ca OE2 3:Glu84 2.39 Ca CD 3:Glu84 3.52 Ca CG 3:Glu84 4.77 Ca O 1:Hoh239 2.28 Ca O 1:Hoh271 4.66 Ca O 3:Hoh228 2.32 Ca O 3:Hoh236 4.36 Ca O 3:Hoh248 4.69 Ca O 3:Hoh249 2.45 Ca O 3:Hoh290 4.58 Ca O 3:Hoh296 4.94 interactive model: