Calcium in the structure of Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed With A Pseudo-Tetraose Derived From Acarbose (pdb 1v3m)

The binding sites of Calcium atom in the structure of Crystal Structure of F283Y Mutant Cyclodextrin Glycosyltransferase Complexed With A Pseudo-Tetraose Derived From Acarbose (pdb code 1v3m). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 1v3m structure was solved by R.KANAI, K.HAGA, T.AKIBA, K.YAMANE, K.HARATA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.0 Space group P1 a (A) 64.090 b (A) 73.600 c (A) 78.300 alpha (°) 84.93 beta (°) 105.12 gamma (°) 101.00 Rfactor (%) 16.3 Rfree (%) 21.8 Calcium Binding Sites: Calcium binding site 1 out of 4 in 1v3m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 1v3m. 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: Asp27, A: Asn29, A: Pro30, A: Asn32, A: Asn33, A: Gly51, A: Gly52, A: Asp53, A: Ala111, A: Hoh1013, A: Hoh1322, conact list: Atom Atom Distance (A) Ca CB A:Asp27 4.42 Ca OD2 A:Asp27 2.48 Ca C A:Asp27 4.97 Ca OD1 A:Asp27 4.08 Ca CG A:Asp27 3.46 Ca CA A:Asp27 4.52 Ca O A:Asn29 2.32 Ca N A:Asn29 4.31 Ca CB A:Asn29 4.75 Ca C A:Asn29 3.48 Ca CA A:Asn29 4.43 Ca O A:Pro30 4.84 Ca N A:Pro30 4.21 Ca C A:Pro30 4.71 Ca CA A:Pro30 4.25 Ca O A:Asn32 4.66 Ca N A:Asn32 4.69 Ca CB A:Asn32 4.56 Ca ND2 A:Asn32 4.10 Ca C A:Asn32 4.29 Ca OD1 A:Asn32 2.17 Ca CG A:Asn32 3.40 Ca CA A:Asn32 4.75 Ca N A:Asn33 4.07 Ca CB A:Asn33 4.42 Ca ND2 A:Asn33 4.20 Ca OD1 A:Asn33 2.11 Ca CG A:Asn33 3.37 Ca CA A:Asn33 4.27 Ca O A:Gly51 2.25 Ca C A:Gly51 3.39 Ca CA A:Gly51 3.96 Ca O A:Gly52 4.74 Ca N A:Gly52 4.49 Ca C A:Gly52 4.56 Ca CA A:Gly52 4.82 Ca N A:Asp53 4.76 Ca CB A:Asp53 3.86 Ca OD2 A:Asp53 2.45 Ca OD1 A:Asp53 4.48 Ca CG A:Asp53 3.45 Ca CA A:Asp53 4.94 Ca O A:Ala111 4.00 Ca O A:Hoh1013 4.75 Ca O A:Hoh1322 2.24 interactive model: Calcium binding site 2 out of 4 in 1v3m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 1v3m. 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: Asn139, A: His176, A: Gly189, A: Ile190, A: Tyr191, A: Lys192, A: Asp199, A: Leu200, A: His233, A: Met234, A: Hoh1496, A: Hoh1497, A: Hoh1498, A: Hoh1649, conact list: Atom Atom Distance (A) Ca O A:Asn139 4.29 Ca CB A:Asn139 4.66 Ca ND2 A:Asn139 4.00 Ca OD1 A:Asn139 2.25 Ca CG A:Asn139 3.43 Ca CA A:Asn139 4.99 Ca ND1 A:His176 4.60 Ca CE1 A:His176 4.76 Ca O A:Gly189 4.58 Ca O A:Ile190 2.43 Ca CG2 A:Ile190 4.76 Ca C A:Ile190 3.56 Ca CA A:Ile190 4.14 Ca N A:Tyr191 4.68 Ca CA A:Tyr191 4.97 Ca O A:Lys192 4.57 Ca CB A:Asp199 4.64 Ca OD2 A:Asp199 2.99 Ca OD1 A:Asp199 2.62 Ca CG A:Asp199 3.17 Ca O A:Leu200 4.77 Ca O A:His233 2.33 Ca CB A:His233 4.48 Ca C A:His233 3.57 Ca CA A:His233 4.55 Ca N A:Met234 4.39 Ca CG A:Met234 4.48 Ca CA A:Met234 4.36 Ca O A:Hoh1496 2.23 Ca O A:Hoh1497 2.29 Ca O A:Hoh1498 4.50 Ca O A:Hoh1649 2.17 interactive model: Calcium binding site 3 out of 4 in 1v3m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 1v3m. 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: Asp27, B: Asn29, B: Pro30, B: Asn32, B: Asn33, B: Gly51, B: Gly52, B: Asp53, B: Ala111, B: Hoh1086, B: Hoh1567, conact list: Atom Atom Distance (A) Ca CB B:Asp27 4.47 Ca OD2 B:Asp27 2.47 Ca OD1 B:Asp27 4.12 Ca CG B:Asp27 3.49 Ca CA B:Asp27 4.56 Ca O B:Asn29 2.30 Ca N B:Asn29 4.34 Ca CB B:Asn29 4.76 Ca C B:Asn29 3.48 Ca CA B:Asn29 4.40 Ca O B:Pro30 4.89 Ca N B:Pro30 4.28 Ca C B:Pro30 4.78 Ca CA B:Pro30 4.33 Ca O B:Asn32 4.69 Ca N B:Asn32 4.75 Ca CB B:Asn32 4.57 Ca ND2 B:Asn32 4.08 Ca C B:Asn32 4.31 Ca OD1 B:Asn32 2.14 Ca CG B:Asn32 3.38 Ca CA B:Asn32 4.79 Ca N B:Asn33 4.07 Ca CB B:Asn33 4.36 Ca ND2 B:Asn33 4.11 Ca OD1 B:Asn33 2.08 Ca CG B:Asn33 3.33 Ca CA B:Asn33 4.22 Ca O B:Gly51 2.21 Ca C B:Gly51 3.35 Ca CA B:Gly51 3.90 Ca O B:Gly52 4.75 Ca N B:Gly52 4.48 Ca C B:Gly52 4.61 Ca CA B:Gly52 4.90 Ca N B:Asp53 4.81 Ca CB B:Asp53 3.81 Ca OD2 B:Asp53 2.41 Ca OD1 B:Asp53 4.36 Ca CG B:Asp53 3.36 Ca CA B:Asp53 4.97 Ca O B:Ala111 3.95 Ca O B:Hoh1086 4.73 Ca O B:Hoh1567 2.11 interactive model: Calcium binding site 4 out of 4 in 1v3m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 1v3m. 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: Asn139, B: His176, B: Gly189, B: Ile190, B: Tyr191, B: Lys192, B: Asp199, B: Leu200, B: His233, B: Met234, B: Hoh1122, B: Hoh1575, B: Hoh1576, B: Hoh1577, conact list: Atom Atom Distance (A) Ca O B:Asn139 4.30 Ca CB B:Asn139 4.68 Ca ND2 B:Asn139 3.97 Ca OD1 B:Asn139 2.25 Ca CG B:Asn139 3.42 Ca ND1 B:His176 4.64 Ca CE1 B:His176 4.86 Ca O B:Gly189 4.63 Ca O B:Ile190 2.40 Ca CG2 B:Ile190 4.83 Ca C B:Ile190 3.57 Ca CA B:Ile190 4.20 Ca N B:Tyr191 4.67 Ca CA B:Tyr191 4.90 Ca O B:Lys192 4.51 Ca CB B:Asp199 4.51 Ca OD2 B:Asp199 2.70 Ca OD1 B:Asp199 2.66 Ca CG B:Asp199 3.03 Ca O B:Leu200 4.63 Ca O B:His233 2.29 Ca CB B:His233 4.46 Ca C B:His233 3.54 Ca CA B:His233 4.53 Ca N B:Met234 4.39 Ca CG B:Met234 4.56 Ca CA B:Met234 4.37 Ca O B:Hoh1122 4.56 Ca O B:Hoh1575 2.30 Ca O B:Hoh1576 2.22 Ca O B:Hoh1577 2.17 interactive model: