Calcium in the structure of Crystal Structure Of The 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form (pdb 1j1e)

The binding sites of Calcium atom in the structure of Crystal Structure Of The 52KDA Domain of Human Cardiac Troponin in the CA2+ Saturated Form (pdb code 1j1e). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 1j1e structure was solved by S.TAKEDA, A.YAMASHITA, K.MAEDA, Y.MAEDA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.3 Space group P1211 a (A) 48.299 b (A) 169.506 c (A) 68.538 alpha (°) 90.00 beta (°) 102.38 gamma (°) 90.00 Rfactor (%) 25.1 Rfree (%) 30.8 Calcium Binding Sites: Calcium binding site 1 out of 6 in 1j1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 1j1e. 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: Asp65, A: Glu66, A: Asp67, A: Ser69, A: Thr71, A: Val72, A: Asp73, A: Glu76, conact list: Atom Atom Distance (A) Ca CB A:Asp65 4.81 Ca OD2 A:Asp65 2.95 Ca OD1 A:Asp65 4.67 Ca CG A:Asp65 3.97 Ca CA A:Asp65 4.62 Ca N A:Glu66 4.44 Ca N A:Asp67 4.17 Ca CB A:Asp67 4.22 Ca OD2 A:Asp67 2.08 Ca C A:Asp67 4.93 Ca OD1 A:Asp67 3.17 Ca CG A:Asp67 2.90 Ca CA A:Asp67 4.66 Ca N A:Ser69 4.28 Ca CB A:Ser69 3.20 Ca OG A:Ser69 2.25 Ca CA A:Ser69 4.35 Ca O A:Thr71 2.91 Ca N A:Thr71 4.83 Ca OG1 A:Thr71 4.77 Ca C A:Thr71 4.12 Ca N A:Val72 4.91 Ca C A:Val72 4.89 Ca CA A:Val72 4.74 Ca N A:Asp73 4.24 Ca CB A:Asp73 4.39 Ca OD2 A:Asp73 3.32 Ca CG A:Asp73 4.14 Ca CA A:Asp73 4.97 Ca OE1 A:Glu76 2.44 Ca CB A:Glu76 5.00 Ca OE2 A:Glu76 2.38 Ca CD A:Glu76 2.73 Ca CG A:Glu76 4.22 interactive model: Calcium binding site 2 out of 6 in 1j1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 1j1e. 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: Asp105, A: Lys106, A: Asn107, A: Ala108, A: Asp109, A: Tyr111, A: Ile112, A: Asp113, A: Glu116, conact list: Atom Atom Distance (A) Ca CB A:Asp105 4.53 Ca C A:Asp105 4.55 Ca OD1 A:Asp105 2.85 Ca CG A:Asp105 4.01 Ca CA A:Asp105 4.22 Ca N A:Lys106 4.44 Ca N A:Asn107 4.11 Ca CB A:Asn107 4.03 Ca ND2 A:Asn107 3.34 Ca C A:Asn107 4.87 Ca OD1 A:Asn107 1.90 Ca CG A:Asn107 2.82 Ca CA A:Asn107 4.57 Ca N A:Ala108 4.90 Ca N A:Asp109 4.60 Ca CB A:Asp109 4.45 Ca OD2 A:Asp109 2.72 Ca OD1 A:Asp109 3.06 Ca CG A:Asp109 3.14 Ca O A:Tyr111 2.54 Ca N A:Tyr111 4.66 Ca CB A:Tyr111 4.97 Ca C A:Tyr111 3.76 Ca CA A:Tyr111 4.73 Ca N A:Ile112 4.60 Ca C A:Ile112 4.75 Ca CA A:Ile112 4.45 Ca N A:Asp113 4.19 Ca CB A:Asp113 4.58 Ca OD2 A:Asp113 4.76 Ca OD1 A:Asp113 3.55 Ca CG A:Asp113 4.10 Ca OE1 A:Glu116 2.17 Ca CB A:Glu116 4.78 Ca OE2 A:Glu116 2.17 Ca CD A:Glu116 2.33 Ca CG A:Glu116 3.68 interactive model: Calcium binding site 3 out of 6 in 1j1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 1j1e. 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: Gly140, A: Asp141, A: Lys142, A: Asn143, A: Asn144, A: Asp145, A: Arg147, A: Ile148, A: Asp149, A: Glu152, conact list: Atom Atom Distance (A) Ca O A:Gly140 4.97 Ca O A:Asp141 4.91 Ca N A:Asp141 4.87 Ca CB A:Asp141 4.01 Ca OD2 A:Asp141 2.04 Ca C A:Asp141 4.31 Ca OD1 A:Asp141 3.96 Ca CG A:Asp141 3.16 Ca CA A:Asp141 3.75 Ca N A:Lys142 4.65 Ca N A:Asn143 4.32 Ca CB A:Asn143 4.17 Ca ND2 A:Asn143 2.73 Ca C A:Asn143 4.81 Ca OD1 A:Asn143 2.27 Ca CG A:Asn143 2.75 Ca CA A:Asn143 4.66 Ca N A:Asn144 4.23 Ca CA A:Asn144 4.94 Ca N A:Asp145 4.13 Ca CB A:Asp145 4.49 Ca OD2 A:Asp145 3.16 Ca OD1 A:Asp145 2.75 Ca CG A:Asp145 3.19 Ca CA A:Asp145 4.84 Ca O A:Arg147 2.52 Ca N A:Arg147 4.72 Ca C A:Arg147 3.65 Ca CA A:Arg147 4.81 Ca N A:Ile148 4.27 Ca C A:Ile148 4.49 Ca CA A:Ile148 4.00 Ca N A:Asp149 4.01 Ca CB A:Asp149 4.89 Ca OD2 A:Asp149 4.06 Ca CG A:Asp149 4.71 Ca OE1 A:Glu152 2.08 Ca CB A:Glu152 4.86 Ca OE2 A:Glu152 2.57 Ca CD A:Glu152 2.62 Ca CG A:Glu152 4.08 interactive model: Calcium binding site 4 out of 6 in 1j1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 1j1e. 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: Asp65, D: Glu66, D: Asp67, D: Gly68, D: Ser69, D: Gly70, D: Thr71, D: Val72, D: Asp73, D: Glu76, conact list: Atom Atom Distance (A) Ca CB D:Asp65 4.11 Ca OD2 D:Asp65 2.25 Ca C D:Asp65 4.53 Ca OD1 D:Asp65 3.61 Ca CG D:Asp65 3.08 Ca CA D:Asp65 4.10 Ca N D:Glu66 4.06 Ca C D:Glu66 4.77 Ca O D:Asp67 4.88 Ca N D:Asp67 3.84 Ca CB D:Asp67 3.95 Ca OD2 D:Asp67 2.00 Ca C D:Asp67 4.24 Ca OD1 D:Asp67 3.33 Ca CG D:Asp67 2.84 Ca CA D:Asp67 4.23 Ca N D:Gly68 4.09 Ca C D:Gly68 4.61 Ca CA D:Gly68 4.76 Ca N D:Ser69 3.62 Ca CB D:Ser69 3.54 Ca OG D:Ser69 2.50 Ca C D:Ser69 4.79 Ca CA D:Ser69 4.14 Ca N D:Gly70 4.81 Ca O D:Thr71 2.78 Ca N D:Thr71 4.50 Ca OG1 D:Thr71 4.41 Ca C D:Thr71 3.80 Ca CA D:Thr71 4.68 Ca N D:Val72 4.60 Ca C D:Val72 4.89 Ca CA D:Val72 4.64 Ca N D:Asp73 4.39 Ca CB D:Asp73 4.81 Ca OD2 D:Asp73 3.01 Ca OD1 D:Asp73 4.32 Ca CG D:Asp73 3.84 Ca OE1 D:Glu76 2.16 Ca CB D:Glu76 4.98 Ca OE2 D:Glu76 2.41 Ca CD D:Glu76 2.59 Ca CG D:Glu76 4.08 interactive model: Calcium binding site 5 out of 6 in 1j1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 1j1e. 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: Asp105, D: Lys106, D: Asn107, D: Ala108, D: Asp109, D: Gly110, D: Tyr111, D: Ile112, D: Asp113, D: Glu116, conact list: Atom Atom Distance (A) Ca CB D:Asp105 4.62 Ca OD2 D:Asp105 2.50 Ca C D:Asp105 4.82 Ca OD1 D:Asp105 4.24 Ca CG D:Asp105 3.60 Ca CA D:Asp105 4.61 Ca N D:Lys106 4.86 Ca N D:Asn107 4.31 Ca CB D:Asn107 4.15 Ca ND2 D:Asn107 2.79 Ca C D:Asn107 4.85 Ca OD1 D:Asn107 2.24 Ca CG D:Asn107 2.76 Ca CA D:Asn107 4.67 Ca N D:Ala108 4.71 Ca N D:Asp109 4.34 Ca CB D:Asp109 4.14 Ca OD2 D:Asp109 3.83 Ca OD1 D:Asp109 2.16 Ca CG D:Asp109 3.16 Ca CA D:Asp109 4.80 Ca N D:Gly110 4.89 Ca O D:Tyr111 2.38 Ca N D:Tyr111 4.29 Ca CB D:Tyr111 4.56 Ca C D:Tyr111 3.58 Ca CA D:Tyr111 4.38 Ca N D:Ile112 4.57 Ca C D:Ile112 4.97 Ca CA D:Ile112 4.68 Ca N D:Asp113 4.35 Ca CB D:Asp113 4.60 Ca OD2 D:Asp113 4.93 Ca OD1 D:Asp113 3.80 Ca CG D:Asp113 4.25 Ca OE1 D:Glu116 2.83 Ca OE2 D:Glu116 2.66 Ca CD D:Glu116 3.03 Ca CG D:Glu116 4.43 interactive model: Calcium binding site 6 out of 6 in 1j1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Calcium in the PDB 1j1e. 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: Asp141, D: Lys142, D: Asn143, D: Asn144, D: Asp145, D: Arg147, D: Ile148, D: Asp149, D: Glu152, conact list: Atom Atom Distance (A) Ca CB D:Asp141 4.99 Ca OD2 D:Asp141 2.99 Ca C D:Asp141 4.76 Ca CG D:Asp141 4.22 Ca CA D:Asp141 4.47 Ca N D:Lys142 4.76 Ca N D:Asn143 4.52 Ca CB D:Asn143 4.53 Ca ND2 D:Asn143 3.37 Ca OD1 D:Asn143 2.23 Ca CG D:Asn143 3.12 Ca CA D:Asn143 4.96 Ca N D:Asn144 4.59 Ca N D:Asp145 4.16 Ca CB D:Asp145 4.26 Ca OD2 D:Asp145 2.45 Ca C D:Asp145 4.90 Ca OD1 D:Asp145 3.22 Ca CG D:Asp145 3.03 Ca CA D:Asp145 4.64 Ca O D:Arg147 2.35 Ca N D:Arg147 4.56 Ca C D:Arg147 3.57 Ca CG D:Arg147 4.66 Ca CA D:Arg147 4.65 Ca N D:Ile148 4.36 Ca C D:Ile148 4.72 Ca CA D:Ile148 4.29 Ca N D:Asp149 4.37 Ca OD2 D:Asp149 4.01 Ca OD1 D:Asp149 3.94 Ca CG D:Asp149 4.17 Ca OE1 D:Glu152 2.55 Ca OE2 D:Glu152 2.53 Ca CD D:Glu152 2.83 Ca CG D:Glu152 4.27 interactive model: