Calcium in the structure of X-Ray Crystallographic Structure of Inorganic Pyrophosphatase At 298K From Archaeon Thermococcus Thioreducens (pdb 3i98)

The binding sites of Calcium atom in the structure of X-Ray Crystallographic Structure of Inorganic Pyrophosphatase At 298K From Archaeon Thermococcus Thioreducens (pdb code 3i98). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 3i98 structure was solved by R.C.HUGHES, L.COATES, E.J.MEEHAN, J.D.NG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 45.2-1.9 Space group C121 a (A) 106.112 b (A) 95.464 c (A) 113.677 alpha (°) 90.00 beta (°) 98.12 gamma (°) 90.00 Rfactor (%) 14.8 Rfree (%) 18.4 Calcium Binding Sites: Calcium binding site 1 out of 6 in 3i98 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 3i98. 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: Asp66, A: Asp68, A: Pro69, A: Asp71, A: Asp103, A: Trp104, A: Lys105, A: Hoh191, A: Hoh193, A: Hoh207, A: Hoh274, A: Hoh435, conact list: Atom Atom Distance (A) Ca CB A:Asp66 4.81 Ca OD2 A:Asp66 2.47 Ca OD1 A:Asp66 3.72 Ca CG A:Asp66 3.45 Ca CB A:Asp68 4.94 Ca O A:Pro69 4.40 Ca N A:Asp71 4.75 Ca N A:Asp71 4.74 Ca CB A:Asp71 4.41 Ca CB A:Asp71 4.51 Ca OD2 A:Asp71 3.61 Ca OD2 A:Asp71 2.36 Ca OD1 A:Asp71 2.40 Ca OD1 A:Asp71 3.49 Ca CG A:Asp71 3.23 Ca O A:Asp103 4.71 Ca CB A:Asp103 4.33 Ca OD2 A:Asp103 4.25 Ca C A:Asp103 4.48 Ca OD1 A:Asp103 2.19 Ca CG A:Asp103 3.42 Ca CA A:Asp103 4.15 Ca O A:Trp104 4.56 Ca NZ A:Lys105 4.16 Ca O A:Hoh191 4.30 Ca O A:Hoh193 2.28 Ca O A:Hoh207 2.37 Ca O A:Hoh274 2.28 Ca O A:Hoh435 4.87 interactive model: Calcium binding site 2 out of 6 in 3i98 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 3i98. 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: Asp66, B: Asp68, B: Pro69, B: Asp71, B: Asp103, B: Trp104, B: Lys105, B: Hoh187, B: Hoh209, B: Hoh216, B: Hoh259, B: Hoh629, conact list: Atom Atom Distance (A) Ca CB B:Asp66 4.80 Ca OD2 B:Asp66 2.45 Ca OD1 B:Asp66 3.68 Ca CG B:Asp66 3.43 Ca CB B:Asp68 4.81 Ca O B:Pro69 4.37 Ca N B:Asp71 4.73 Ca CB B:Asp71 4.41 Ca CB B:Asp71 4.42 Ca OD2 B:Asp71 2.52 Ca OD2 B:Asp71 2.91 Ca OD1 B:Asp71 2.57 Ca OD1 B:Asp71 4.10 Ca CG B:Asp71 2.89 Ca CG B:Asp71 3.58 Ca O B:Asp103 4.82 Ca CB B:Asp103 4.33 Ca OD2 B:Asp103 4.27 Ca C B:Asp103 4.52 Ca OD1 B:Asp103 2.21 Ca CG B:Asp103 3.44 Ca CA B:Asp103 4.16 Ca O B:Trp104 4.50 Ca NZ B:Lys105 4.27 Ca O B:Hoh187 2.32 Ca O B:Hoh209 4.23 Ca O B:Hoh216 2.45 Ca O B:Hoh259 4.17 Ca O B:Hoh629 2.27 interactive model: Calcium binding site 3 out of 6 in 3i98 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 3i98. 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: Asp66, C: Asp68, C: Pro69, C: Asp71, C: Asp103, C: Trp104, C: Lys105, C: Hoh184, C: Hoh196, C: Hoh243, C: Hoh400, C: Hoh587, conact list: Atom Atom Distance (A) Ca CB C:Asp66 4.78 Ca OD2 C:Asp66 2.50 Ca OD1 C:Asp66 3.72 Ca CG C:Asp66 3.45 Ca CB C:Asp68 4.79 Ca O C:Pro69 4.35 Ca N C:Asp71 4.77 Ca CB C:Asp71 4.52 Ca OD2 C:Asp71 2.53 Ca OD1 C:Asp71 3.91 Ca CG C:Asp71 3.43 Ca O C:Asp103 4.70 Ca CB C:Asp103 4.36 Ca OD2 C:Asp103 4.32 Ca C C:Asp103 4.50 Ca OD1 C:Asp103 2.25 Ca CG C:Asp103 3.48 Ca CA C:Asp103 4.18 Ca O C:Trp104 4.52 Ca NZ C:Lys105 4.16 Ca O C:Hoh184 4.34 Ca O C:Hoh196 2.37 Ca O C:Hoh243 2.33 Ca O C:Hoh400 2.24 Ca O C:Hoh587 4.13 interactive model: Calcium binding site 4 out of 6 in 3i98 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 3i98. 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: Asp66, D: Asp68, D: Pro69, D: Asp71, D: Asp103, D: Trp104, D: Lys105, D: Hoh195, D: Hoh205, D: Hoh226, D: Hoh479, D: Hoh562, conact list: Atom Atom Distance (A) Ca CB D:Asp66 4.93 Ca OD2 D:Asp66 2.60 Ca OD1 D:Asp66 3.90 Ca CG D:Asp66 3.60 Ca CB D:Asp68 4.61 Ca O D:Pro69 4.37 Ca N D:Asp71 4.87 Ca CB D:Asp71 4.53 Ca OD2 D:Asp71 2.72 Ca OD1 D:Asp71 4.04 Ca CG D:Asp71 3.54 Ca O D:Asp103 4.66 Ca CB D:Asp103 4.40 Ca OD2 D:Asp103 4.33 Ca C D:Asp103 4.53 Ca OD1 D:Asp103 2.32 Ca CG D:Asp103 3.52 Ca CA D:Asp103 4.24 Ca O D:Trp104 4.61 Ca NZ D:Lys105 4.23 Ca O D:Hoh195 4.07 Ca O D:Hoh205 2.47 Ca O D:Hoh226 2.63 Ca O D:Hoh479 4.31 Ca O D:Hoh562 2.25 interactive model: Calcium binding site 5 out of 6 in 3i98 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 3i98. 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: Asp66, E: Asp68, E: Pro69, E: Asp71, E: Asp103, E: Trp104, E: Lys105, E: Hoh196, E: Hoh224, E: Hoh312, E: Hoh388, E: Hoh638, conact list: Atom Atom Distance (A) Ca CB E:Asp66 4.76 Ca OD2 E:Asp66 2.47 Ca OD1 E:Asp66 3.65 Ca CG E:Asp66 3.41 Ca CB E:Asp68 4.67 Ca O E:Pro69 4.38 Ca N E:Asp71 4.88 Ca CB E:Asp71 4.55 Ca OD2 E:Asp71 2.47 Ca OD1 E:Asp71 3.90 Ca CG E:Asp71 3.42 Ca O E:Asp103 4.85 Ca CB E:Asp103 4.50 Ca OD2 E:Asp103 4.31 Ca C E:Asp103 4.66 Ca OD1 E:Asp103 2.31 Ca CG E:Asp103 3.54 Ca CA E:Asp103 4.34 Ca O E:Trp104 4.72 Ca NZ E:Lys105 4.16 Ca O E:Hoh196 2.40 Ca O E:Hoh224 4.21 Ca O E:Hoh312 2.55 Ca O E:Hoh388 2.35 Ca O E:Hoh638 4.85 interactive model: Calcium binding site 6 out of 6 in 3i98 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Calcium in the PDB 3i98. 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: F: Asp66, F: Asp68, F: Pro69, F: Asp71, F: Asp103, F: Trp104, F: Lys105, F: Hoh199, F: Hoh229, F: Hoh304, F: Hoh323, F: Hoh332, conact list: Atom Atom Distance (A) Ca CB F:Asp66 4.70 Ca OD2 F:Asp66 2.37 Ca OD1 F:Asp66 3.72 Ca CG F:Asp66 3.39 Ca CB F:Asp68 4.77 Ca O F:Pro69 4.38 Ca N F:Asp71 4.89 Ca CB F:Asp71 4.50 Ca OD2 F:Asp71 2.52 Ca OD1 F:Asp71 3.71 Ca CG F:Asp71 3.34 Ca O F:Asp103 4.78 Ca CB F:Asp103 4.36 Ca OD2 F:Asp103 4.29 Ca C F:Asp103 4.59 Ca OD1 F:Asp103 2.21 Ca CG F:Asp103 3.45 Ca CA F:Asp103 4.24 Ca O F:Trp104 4.65 Ca NZ F:Lys105 4.21 Ca O F:Hoh199 2.49 Ca O F:Hoh229 2.45 Ca O F:Hoh304 2.17 Ca O F:Hoh323 4.24 Ca O F:Hoh332 4.87 interactive model: