Cobalt in the structure of Crystal Structure of Cobalt(II)-D(Ggcgcc)2 (pdb 1p24)

The binding sites of Cobalt atom in the structure of Crystal Structure of Cobalt(II)-D(Ggcgcc)2 (pdb code 1p24). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 1p24 structure was solved by S.L.LABIUK, L.T.DELBAERE, J.S.LEE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-3.0 Space group P41212 a (A) 68.940 b (A) 68.940 c (A) 55.270 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.7 Rfree (%) 28.6 Cobalt Binding Sites: Cobalt binding site 1 out of 5 in 1p24 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 1p24. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg1, A: Dg2, A: Hoh201, A: Hoh202, A: Hoh203, A: Hoh204, A: Hoh205, conact list: Atom Atom Distance (A) Co N9 A:Dg1 4.26 Co C8 A:Dg1 3.03 Co C6 A:Dg1 3.74 Co C5 A:Dg1 3.16 Co N7 A:Dg1 2.10 Co C4 A:Dg1 4.29 Co O6 A:Dg1 3.61 Co O6 A:Dg2 4.81 Co O A:Hoh201 2.12 Co O A:Hoh202 2.11 Co O A:Hoh203 2.14 Co O A:Hoh204 2.13 Co O A:Hoh205 2.12 interactive model: Cobalt binding site 2 out of 5 in 1p24 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 1p24. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dc6, B: Dg7, B: Hoh206, B: Hoh207, B: Hoh208, B: Hoh209, B: Hoh210, conact list: Atom Atom Distance (A) Co N4 A:Dc6 4.69 Co N9 B:Dg7 4.22 Co C8 B:Dg7 3.02 Co C6 B:Dg7 3.64 Co N1 B:Dg7 4.99 Co C5 B:Dg7 3.12 Co N7 B:Dg7 2.09 Co C4 B:Dg7 4.24 Co O6 B:Dg7 3.46 Co O B:Hoh206 2.13 Co O B:Hoh207 2.13 Co O B:Hoh208 2.12 Co O B:Hoh209 2.13 Co O B:Hoh210 2.14 interactive model: Cobalt binding site 3 out of 5 in 1p24 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 1p24. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Dg13, C: Dg14, C: Hoh211, C: Hoh212, C: Hoh213, C: Hoh214, C: Hoh215, conact list: Atom Atom Distance (A) Co N9 C:Dg13 4.30 Co C8 C:Dg13 3.11 Co C6 C:Dg13 3.54 Co N1 C:Dg13 4.90 Co C5 C:Dg13 3.10 Co N7 C:Dg13 2.10 Co C4 C:Dg13 4.28 Co O6 C:Dg13 3.28 Co N7 C:Dg14 4.80 Co O6 C:Dg14 4.71 Co O C:Hoh211 2.12 Co O C:Hoh212 2.12 Co O C:Hoh213 2.13 Co O C:Hoh214 2.13 Co O C:Hoh215 2.12 interactive model: Cobalt binding site 4 out of 5 in 1p24 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 1p24. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Dg19, D: Dg20, D: Hoh216, D: Hoh217, D: Hoh218, D: Hoh219, D: Hoh220, conact list: Atom Atom Distance (A) Co N9 D:Dg19 4.02 Co C8 D:Dg19 2.88 Co C6 D:Dg19 3.74 Co C5 D:Dg19 3.11 Co N7 D:Dg19 2.09 Co C4 D:Dg19 4.13 Co O6 D:Dg19 3.66 Co N7 D:Dg20 4.88 Co O6 D:Dg20 4.51 Co O D:Hoh216 2.12 Co O D:Hoh217 2.12 Co O D:Hoh218 2.14 Co O D:Hoh219 2.14 Co O D:Hoh220 2.14 interactive model: Cobalt binding site 5 out of 5 in 1p24 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 1p24. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: Dg25, E: Hoh221, E: Hoh222, E: Hoh223, E: Hoh224, E: Hoh225, conact list: Atom Atom Distance (A) Co N9 E:Dg25 4.31 Co C8 E:Dg25 3.06 Co C6 E:Dg25 3.89 Co C5 E:Dg25 3.31 Co N7 E:Dg25 2.16 Co C4 E:Dg25 4.42 Co O6 E:Dg25 3.72 Co O E:Hoh221 2.13 Co O E:Hoh222 2.13 Co O E:Hoh223 2.12 Co O E:Hoh224 2.12 Co O E:Hoh225 2.12 interactive model: