Cobalt in the structure of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, With Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au) (pdb 2fij)

The binding sites of Cobalt atom in the structure of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, With Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au) (pdb code 2fij). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 2fij structure was solved by M.EGLI, F.LI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 33.4-1.2 Space group P212121 a (A) 32.277 b (A) 32.469 c (A) 66.749 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.7 Rfree (%) 16.9 Cobalt Binding Sites: Cobalt binding site 1 out of 3 in 2fij Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 2fij. 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: Dc2, A: Dg3, B: Dc12, B: Dg13, A: Nco2211, A: Hoh123, A: Hoh183, A: Hoh186, B: Hoh170, conact list: Atom Atom Distance (A) Co OP1 A:Dc2 3.85 Co OP1 A:Dg3 4.50 Co P A:Dg3 4.96 Co OP2 A:Dg3 4.55 Co OP1 B:Dc12 3.86 Co OP1 B:Dg13 4.48 Co P B:Dg13 4.94 Co OP2 B:Dg13 4.46 Co N1 A:Nco2211 1.99 Co N6 A:Nco2211 1.97 Co CO A:Nco2211 0.00 Co N3 A:Nco2211 1.99 Co N2 A:Nco2211 1.98 Co N5 A:Nco2211 1.98 Co N4 A:Nco2211 1.98 Co O A:Hoh123 4.19 Co O A:Hoh183 4.25 Co O A:Hoh186 4.10 Co O B:Hoh170 4.13 interactive model: Cobalt binding site 2 out of 3 in 2fij Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 2fij. 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: Dg3, A: Dt4, B: Uar16, A: Cl101, A: Nco2213, A: Hoh102, A: Hoh110, A: Hoh140, A: Hoh146, A: Hoh182, B: Hoh111, B: Hoh148, B: Hoh169, B: Hoh174, B: Hoh228, conact list: Atom Atom Distance (A) Co C6 A:Dg3 4.99 Co N7 A:Dg3 4.34 Co O6 A:Dg3 4.29 Co O4 A:Dt4 4.66 Co O4 B:Uar16 4.84 Co CL A:Cl101 4.19 Co N1 A:Nco2213 1.99 Co N6 A:Nco2213 1.98 Co CO A:Nco2213 0.00 Co N3 A:Nco2213 1.98 Co N2 A:Nco2213 1.98 Co N5 A:Nco2213 1.99 Co N4 A:Nco2213 1.98 Co O A:Hoh102 3.96 Co O A:Hoh110 4.22 Co O A:Hoh140 4.65 Co O A:Hoh146 4.62 Co O A:Hoh182 4.33 Co O B:Hoh111 4.22 Co O B:Hoh148 4.41 Co O B:Hoh169 4.90 Co O B:Hoh174 3.74 Co O B:Hoh228 4.09 interactive model: Cobalt binding site 3 out of 3 in 2fij Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 2fij. 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: Uar6, B: Dg13, B: Dt14, A: Cl101, B: Nco2212, A: Hoh106, A: Hoh129, A: Hoh140, A: Hoh160, A: Hoh218, B: Hoh104, B: Hoh130, B: Hoh158, B: Hoh159, B: Hoh205, conact list: Atom Atom Distance (A) Co O4 A:Uar6 4.90 Co C6 B:Dg13 4.96 Co C5 B:Dg13 4.99 Co N7 B:Dg13 4.33 Co O6 B:Dg13 4.26 Co O4 B:Dt14 4.64 Co CL A:Cl101 4.17 Co N1 B:Nco2212 1.98 Co N6 B:Nco2212 1.98 Co CO B:Nco2212 0.00 Co N3 B:Nco2212 1.99 Co N2 B:Nco2212 1.98 Co N5 B:Nco2212 1.98 Co N4 B:Nco2212 1.98 Co O A:Hoh106 4.21 Co O A:Hoh129 4.38 Co O A:Hoh140 4.91 Co O A:Hoh160 3.95 Co O A:Hoh218 4.09 Co O B:Hoh104 4.01 Co O B:Hoh130 4.40 Co O B:Hoh158 4.33 Co O B:Hoh159 4.36 Co O B:Hoh205 4.91 interactive model: