Calcium in the structure of The 1.0 Angstrom Crystal Structure of Ca+2 Bound Calmodulin (pdb 1exr)

The binding sites of Calcium atom in the structure of The 1.0 Angstrom Crystal Structure of Ca+2 Bound Calmodulin (pdb code 1exr). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 1exr structure was solved by M.A.WILSON, A.T.BRUNGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 500.0-1.0 Space group P1 a (A) 25.015 b (A) 29.415 c (A) 52.761 alpha (°) 89.54 beta (°) 86.10 gamma (°) 82.39 Rfactor (%) 13.4 Rfree (%) 16.3 Calcium Binding Sites: Calcium binding site 1 out of 5 in 1exr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 1exr. 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: Asp20, A: Lys21, A: Asp22, A: Gly23, A: Asp24, A: Gly25, A: Thr26, A: Ile27, A: Thr28, A: Glu31, A: Hoh2041, A: Hoh2042, A: Hoh2047, A: Hoh2122, conact list: Atom Atom Distance (A) Ca O A:Asp20 4.91 Ca CB A:Asp20 4.21 Ca OD2 A:Asp20 4.25 Ca C A:Asp20 4.35 Ca OD1 A:Asp20 2.31 Ca CG A:Asp20 3.41 Ca CA A:Asp20 4.07 Ca N A:Lys21 4.55 Ca N A:Asp22 4.33 Ca CB A:Asp22 4.66 Ca OD2 A:Asp22 4.11 Ca C A:Asp22 4.82 Ca OD1 A:Asp22 2.44 Ca CG A:Asp22 3.53 Ca CA A:Asp22 4.77 Ca N A:Gly23 4.57 Ca N A:Asp24 4.12 Ca CB A:Asp24 4.27 Ca OD2 A:Asp24 3.99 Ca C A:Asp24 4.91 Ca OD1 A:Asp24 2.35 Ca CG A:Asp24 3.34 Ca CA A:Asp24 4.60 Ca N A:Gly25 4.87 Ca O A:Thr26 2.35 Ca N A:Thr26 4.17 Ca CB A:Thr26 4.76 Ca OG1 A:Thr26 3.93 Ca C A:Thr26 3.52 Ca CA A:Thr26 4.36 Ca N A:Ile27 4.47 Ca CA A:Ile27 4.61 Ca N A:Thr28 4.96 Ca OE1 A:Glu31 2.47 Ca OE2 A:Glu31 2.48 Ca CD A:Glu31 2.82 Ca CG A:Glu31 4.31 Ca O A:Hoh2041 4.50 Ca O A:Hoh2042 4.60 Ca O A:Hoh2047 4.85 Ca O A:Hoh2122 2.35 interactive model: Calcium binding site 2 out of 5 in 1exr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 1exr. 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: Asp56, A: Ala57, A: Asp58, A: Gly59, A: Asn60, A: Gly61, A: Thr62, A: Ile63, A: Asp64, A: Glu67, A: Hoh2008, A: Hoh2011, A: Hoh2127, conact list: Atom Atom Distance (A) Ca CB A:Asp56 4.31 Ca OD2 A:Asp56 4.27 Ca C A:Asp56 4.58 Ca OD1 A:Asp56 2.34 Ca CG A:Asp56 3.43 Ca CA A:Asp56 4.35 Ca N A:Ala57 4.66 Ca N A:Asp58 4.33 Ca CB A:Asp58 4.64 Ca OD2 A:Asp58 3.86 Ca C A:Asp58 4.98 Ca OD1 A:Asp58 2.43 Ca CG A:Asp58 3.42 Ca CA A:Asp58 4.86 Ca N A:Gly59 4.68 Ca N A:Asn60 4.35 Ca CB A:Asn60 4.52 Ca ND2 A:Asn60 3.78 Ca OD1 A:Asn60 2.40 Ca CG A:Asn60 3.32 Ca CA A:Asn60 4.84 Ca N A:Gly61 4.89 Ca O A:Thr62 2.41 Ca N A:Thr62 4.35 Ca OG1 A:Thr62 4.50 Ca C A:Thr62 3.58 Ca CA A:Thr62 4.55 Ca N A:Ile63 4.40 Ca C A:Ile63 4.84 Ca CA A:Ile63 4.39 Ca N A:Asp64 4.47 Ca OD2 A:Asp64 4.71 Ca CG A:Asp64 4.81 Ca OE1 A:Glu67 2.47 Ca OE2 A:Glu67 2.60 Ca CD A:Glu67 2.88 Ca CG A:Glu67 4.40 Ca O A:Hoh2008 4.82 Ca O A:Hoh2011 2.90 Ca O A:Hoh2127 2.42 interactive model: Calcium binding site 3 out of 5 in 1exr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 1exr. 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: Asp129, A: Ile130, A: Asp131, A: Gly132, A: Asp133, A: Gly134, A: His135, A: Ile136, A: Asn137, A: Glu140, A: Hoh2129, conact list: Atom Atom Distance (A) Ca CB A:Asp129 4.43 Ca OD2 A:Asp129 4.16 Ca C A:Asp129 4.92 Ca OD1 A:Asp129 2.30 Ca CG A:Asp129 3.45 Ca CA A:Asp129 4.41 Ca N A:Ile130 4.46 Ca N A:Asp131 4.29 Ca CB A:Asp131 4.47 Ca OD2 A:Asp131 3.53 Ca C A:Asp131 4.77 Ca OD1 A:Asp131 2.34 Ca CG A:Asp131 3.21 Ca CA A:Asp131 4.69 Ca N A:Gly132 4.42 Ca N A:Asp133 4.13 Ca CB A:Asp133 4.40 Ca OD2 A:Asp133 3.80 Ca C A:Asp133 4.86 Ca OD1 A:Asp133 2.38 Ca CG A:Asp133 3.29 Ca CA A:Asp133 4.67 Ca N A:Gly134 4.70 Ca O A:His135 2.35 Ca N A:His135 4.16 Ca CB A:His135 4.74 Ca C A:His135 3.47 Ca CA A:His135 4.35 Ca N A:Ile136 4.33 Ca N A:Ile136 4.32 Ca CD1 A:Ile136 4.87 Ca C A:Ile136 4.84 Ca C A:Ile136 4.86 Ca CA A:Ile136 4.37 Ca CA A:Ile136 4.39 Ca N A:Asn137 4.40 Ca OE1 A:Glu140 2.44 Ca OE2 A:Glu140 2.55 Ca CD A:Glu140 2.87 Ca CG A:Glu140 4.37 Ca O A:Hoh2129 2.42 interactive model: Calcium binding site 4 out of 5 in 1exr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 1exr. 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: Asn42, A: Pro43, A: Thr44, A: Glu47, A: Hoh2018, A: Hoh2083, A: Hoh2123, A: Hoh2124, A: Hoh2125, A: Hoh2126, A: Hoh2146, A: Hoh2176, conact list: Atom Atom Distance (A) Ca O A:Asn42 4.74 Ca CA A:Pro43 4.56 Ca CA A:Pro43 4.36 Ca N A:Thr44 4.70 Ca CG2 A:Thr44 4.81 Ca OE1 A:Glu47 2.50 Ca OE2 A:Glu47 2.45 Ca CD A:Glu47 2.82 Ca CG A:Glu47 4.30 Ca O A:Hoh2018 4.88 Ca O A:Hoh2083 4.53 Ca O A:Hoh2123 2.41 Ca O A:Hoh2124 2.41 Ca O A:Hoh2125 2.40 Ca O A:Hoh2126 2.36 Ca O A:Hoh2146 4.84 Ca O A:Hoh2176 4.91 interactive model: Calcium binding site 5 out of 5 in 1exr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 1exr. 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: Asp93, A: Arg94, A: Asp95, A: Gly96, A: Asn97, A: Gly98, A: Leu99, A: Ile100, A: Ser101, A: Glu104, A: Hoh2081, A: Hoh2128, conact list: Atom Atom Distance (A) Ca O A:Asp93 4.90 Ca CB A:Asp93 4.42 Ca OD2 A:Asp93 4.28 Ca C A:Asp93 4.39 Ca OD1 A:Asp93 2.30 Ca CG A:Asp93 3.48 Ca CA A:Asp93 4.31 Ca N A:Arg94 4.55 Ca N A:Asp95 4.24 Ca CB A:Asp95 4.46 Ca OD2 A:Asp95 3.77 Ca C A:Asp95 4.79 Ca OD1 A:Asp95 2.33 Ca CG A:Asp95 3.29 Ca CA A:Asp95 4.68 Ca N A:Gly96 4.56 Ca N A:Asn97 4.16 Ca CB A:Asn97 4.42 Ca ND2 A:Asn97 4.08 Ca C A:Asn97 4.96 Ca OD1 A:Asn97 2.42 Ca CG A:Asn97 3.42 Ca CA A:Asn97 4.70 Ca N A:Gly98 4.81 Ca O A:Leu99 2.28 Ca N A:Leu99 4.18 Ca CB A:Leu99 4.72 Ca C A:Leu99 3.49 Ca CA A:Leu99 4.33 Ca N A:Ile100 4.39 Ca N A:Ile100 4.43 Ca CD1 A:Ile100 4.86 Ca C A:Ile100 4.91 Ca C A:Ile100 4.97 Ca CA A:Ile100 4.43 Ca CA A:Ile100 4.51 Ca N A:Ser101 4.50 Ca OE1 A:Glu104 2.46 Ca OE2 A:Glu104 2.54 Ca CD A:Glu104 2.84 Ca CG A:Glu104 4.34 Ca O A:Hoh2081 4.50 Ca O A:Hoh2128 2.37 interactive model: