Calcium in the structure of Crystal Structure Of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex With Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate (pdb 1sk6)

The binding sites of Calcium atom in the structure of Crystal Structure Of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex With Calmodulin, 3',5' Cyclic Amp (Camp), and Pyrophosphate (pdb code 1sk6). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 1sk6 structure was solved by Q.GUO, Y.SHEN, N.L.ZHUKOVSKAYA, W.J.TANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-3.2 Space group I222 a (A) 116.870 b (A) 166.453 c (A) 342.393 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 25 Rfree (%) 30.7 Calcium Binding Sites: Calcium binding site 1 out of 6 in 1sk6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 1sk6. 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: Asp129, D: Ile130, D: Asp131, D: Gly132, D: Asp133, D: Gly134, D: Gln135, D: Val136, D: Asn137, D: Glu140, conact list: Atom Atom Distance (A) Ca CB D:Asp129 4.32 Ca OD2 D:Asp129 3.33 Ca C D:Asp129 4.80 Ca OD1 D:Asp129 2.67 Ca CG D:Asp129 3.17 Ca CA D:Asp129 4.39 Ca N D:Ile130 4.15 Ca N D:Asp131 4.19 Ca CB D:Asp131 4.40 Ca OD2 D:Asp131 3.38 Ca C D:Asp131 4.73 Ca OD1 D:Asp131 2.06 Ca CG D:Asp131 3.06 Ca CA D:Asp131 4.69 Ca N D:Gly132 4.15 Ca C D:Gly132 4.82 Ca CA D:Gly132 4.80 Ca N D:Asp133 3.87 Ca CB D:Asp133 4.35 Ca OD2 D:Asp133 2.73 Ca OD1 D:Asp133 3.36 Ca CG D:Asp133 3.21 Ca CA D:Asp133 4.59 Ca N D:Gly134 4.65 Ca O D:Gln135 2.28 Ca N D:Gln135 4.26 Ca C D:Gln135 3.41 Ca CA D:Gln135 4.49 Ca N D:Val136 4.13 Ca C D:Val136 4.66 Ca CA D:Val136 4.01 Ca N D:Asn137 4.37 Ca ND2 D:Asn137 4.96 Ca OE1 D:Glu140 2.40 Ca OE2 D:Glu140 2.39 Ca CD D:Glu140 2.72 Ca CG D:Glu140 4.23 interactive model: Calcium binding site 2 out of 6 in 1sk6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 1sk6. 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: Asp93, D: Asp95, D: Gly96, D: Asn97, D: Gly98, D: Tyr99, D: Ile100, D: Ser101, D: Glu104, conact list: Atom Atom Distance (A) Ca O D:Asp93 4.97 Ca CB D:Asp93 4.31 Ca OD2 D:Asp93 4.16 Ca C D:Asp93 4.73 Ca OD1 D:Asp93 2.11 Ca CG D:Asp93 3.36 Ca CA D:Asp93 4.34 Ca N D:Asp95 4.50 Ca CB D:Asp95 3.63 Ca OD2 D:Asp95 1.74 Ca C D:Asp95 5.00 Ca OD1 D:Asp95 1.89 Ca CG D:Asp95 2.10 Ca CA D:Asp95 4.56 Ca N D:Gly96 4.57 Ca N D:Asn97 4.12 Ca CB D:Asn97 3.77 Ca ND2 D:Asn97 2.36 Ca C D:Asn97 4.90 Ca OD1 D:Asn97 1.65 Ca CG D:Asn97 2.27 Ca CA D:Asn97 4.43 Ca N D:Gly98 4.68 Ca O D:Tyr99 2.14 Ca N D:Tyr99 4.27 Ca C D:Tyr99 3.34 Ca CA D:Tyr99 4.39 Ca N D:Ile100 4.16 Ca C D:Ile100 4.49 Ca CA D:Ile100 4.14 Ca N D:Ser101 4.23 Ca CB D:Ser101 4.74 Ca OG D:Ser101 4.66 Ca OE1 D:Glu104 1.78 Ca CB D:Glu104 4.60 Ca OE2 D:Glu104 2.02 Ca CD D:Glu104 2.06 Ca CG D:Glu104 3.45 interactive model: Calcium binding site 3 out of 6 in 1sk6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 1sk6. 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: Asp129, E: Ile130, E: Asp131, E: Gly132, E: Asp133, E: Gly134, E: Gln135, E: Val136, E: Asn137, E: Glu140, conact list: Atom Atom Distance (A) Ca CB E:Asp129 4.28 Ca OD2 E:Asp129 3.30 Ca C E:Asp129 4.76 Ca OD1 E:Asp129 3.66 Ca CG E:Asp129 3.48 Ca CA E:Asp129 4.20 Ca N E:Ile130 4.20 Ca N E:Asp131 4.49 Ca CB E:Asp131 4.88 Ca OD2 E:Asp131 3.45 Ca OD1 E:Asp131 3.13 Ca CG E:Asp131 3.56 Ca N E:Gly132 4.79 Ca N E:Asp133 4.48 Ca CB E:Asp133 4.17 Ca OD2 E:Asp133 2.39 Ca OD1 E:Asp133 2.41 Ca CG E:Asp133 2.69 Ca CA E:Asp133 4.80 Ca N E:Gly134 4.86 Ca O E:Gln135 2.32 Ca N E:Gln135 4.36 Ca C E:Gln135 3.54 Ca CA E:Gln135 4.59 Ca N E:Val136 4.31 Ca C E:Val136 4.80 Ca CA E:Val136 4.13 Ca N E:Asn137 4.41 Ca ND2 E:Asn137 4.17 Ca CG E:Asn137 4.97 Ca OE1 E:Glu140 2.08 Ca CB E:Glu140 4.92 Ca OE2 E:Glu140 2.53 Ca CD E:Glu140 2.58 Ca CG E:Glu140 4.04 interactive model: Calcium binding site 4 out of 6 in 1sk6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 1sk6. 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: Asp93, E: Asp95, E: Gly96, E: Asn97, E: Gly98, E: Tyr99, E: Ile100, E: Ser101, E: Glu104, conact list: Atom Atom Distance (A) Ca O E:Asp93 4.88 Ca CB E:Asp93 4.38 Ca OD2 E:Asp93 4.16 Ca C E:Asp93 4.74 Ca OD1 E:Asp93 2.21 Ca CG E:Asp93 3.40 Ca CA E:Asp93 4.39 Ca N E:Asp95 4.71 Ca CB E:Asp95 4.06 Ca OD2 E:Asp95 2.59 Ca OD1 E:Asp95 1.88 Ca CG E:Asp95 2.56 Ca CA E:Asp95 4.83 Ca N E:Gly96 4.57 Ca N E:Asn97 3.98 Ca CB E:Asn97 3.57 Ca ND2 E:Asn97 1.98 Ca C E:Asn97 4.55 Ca OD1 E:Asn97 1.91 Ca CG E:Asn97 2.13 Ca CA E:Asn97 4.23 Ca N E:Gly98 4.42 Ca C E:Gly98 4.88 Ca O E:Tyr99 1.81 Ca N E:Tyr99 3.74 Ca CB E:Tyr99 4.33 Ca C E:Tyr99 3.01 Ca CA E:Tyr99 3.84 Ca N E:Ile100 4.04 Ca C E:Ile100 4.91 Ca CA E:Ile100 4.26 Ca N E:Ser101 4.58 Ca OE1 E:Glu104 2.06 Ca CB E:Glu104 4.94 Ca OE2 E:Glu104 2.32 Ca CD E:Glu104 2.50 Ca CG E:Glu104 3.99 interactive model: Calcium binding site 5 out of 6 in 1sk6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 1sk6. 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: Asp129, F: Ile130, F: Asp131, F: Asp133, F: Gly134, F: Gln135, F: Val136, F: Asn137, F: Glu140, conact list: Atom Atom Distance (A) Ca CB F:Asp129 4.33 Ca OD2 F:Asp129 3.60 Ca C F:Asp129 4.87 Ca OD1 F:Asp129 3.41 Ca CG F:Asp129 3.51 Ca CA F:Asp129 4.28 Ca N F:Ile130 4.37 Ca N F:Asp131 4.62 Ca OD2 F:Asp131 4.10 Ca OD1 F:Asp131 2.98 Ca CG F:Asp131 3.86 Ca N F:Asp133 4.72 Ca CB F:Asp133 4.04 Ca OD2 F:Asp133 2.26 Ca OD1 F:Asp133 2.20 Ca CG F:Asp133 2.53 Ca CA F:Asp133 4.86 Ca N F:Gly134 4.73 Ca O F:Gln135 2.15 Ca N F:Gln135 4.18 Ca CB F:Gln135 4.99 Ca C F:Gln135 3.33 Ca CG F:Gln135 4.51 Ca CA F:Gln135 4.38 Ca N F:Val136 4.11 Ca C F:Val136 4.44 Ca CA F:Val136 4.00 Ca N F:Asn137 3.85 Ca CB F:Asn137 4.86 Ca ND2 F:Asn137 4.63 Ca CG F:Asn137 4.85 Ca CA F:Asn137 4.95 Ca OE1 F:Glu140 2.19 Ca CB F:Glu140 4.92 Ca OE2 F:Glu140 2.59 Ca CD F:Glu140 2.68 Ca CG F:Glu140 4.12 interactive model: Calcium binding site 6 out of 6 in 1sk6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Calcium in the PDB 1sk6. 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: Asp93, F: Asp95, F: Gly96, F: Asn97, F: Gly98, F: Tyr99, F: Ile100, F: Ser101, F: Glu104, conact list: Atom Atom Distance (A) Ca CB F:Asp93 4.19 Ca OD2 F:Asp93 3.58 Ca C F:Asp93 4.96 Ca OD1 F:Asp93 1.82 Ca CG F:Asp93 2.99 Ca CA F:Asp93 4.47 Ca N F:Asp95 4.33 Ca CB F:Asp95 3.46 Ca OD2 F:Asp95 1.67 Ca C F:Asp95 4.69 Ca OD1 F:Asp95 1.72 Ca CG F:Asp95 1.94 Ca CA F:Asp95 4.36 Ca N F:Gly96 4.53 Ca N F:Asn97 4.11 Ca CB F:Asn97 3.60 Ca ND2 F:Asn97 2.07 Ca C F:Asn97 4.82 Ca OD1 F:Asn97 1.65 Ca CG F:Asn97 2.08 Ca CA F:Asn97 4.36 Ca N F:Gly98 4.45 Ca O F:Tyr99 1.77 Ca N F:Tyr99 3.86 Ca CB F:Tyr99 4.55 Ca C F:Tyr99 2.99 Ca CA F:Tyr99 3.96 Ca N F:Ile100 3.92 Ca C F:Ile100 4.59 Ca CA F:Ile100 4.07 Ca N F:Ser101 4.22 Ca OE1 F:Glu104 1.73 Ca CB F:Glu104 4.95 Ca OE2 F:Glu104 2.68 Ca CD F:Glu104 2.48 Ca CG F:Glu104 3.90 interactive model: