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 |
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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 |
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