Cobalt in the structure of Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating The ADE38DAP Mutation and A 2',5' Phosphodiester Linkage At the Active Site (pdb 3b5f)

The binding sites of Cobalt atom in the structure of Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating The ADE38DAP Mutation and A 2',5' Phosphodiester Linkage At the Active Site (pdb code 3b5f). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 3b5f structure was solved by C.MACELREVEY, J.KRUCINSKA, J.E.WEDEKIND, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 38.3-2.7 Space group P6122 a (A) 93.490 b (A) 93.490 c (A) 133.820 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 22.3 Rfree (%) 25 Cobalt Binding Sites: Cobalt binding site 1 out of 2 in 3b5f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 3b5f. 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: B: A20, B: G21, C: A40, C: U41, B: Nco101, conact list: Atom Atom Distance (A) Co OP2 B:A20 3.99 Co C6 B:G21 4.89 Co N7 B:G21 4.32 Co O6 B:G21 4.06 Co OP1 C:A40 3.81 Co P C:A40 4.66 Co OP2 C:A40 4.62 Co OP2 C:U41 3.81 Co N1 B:Nco101 2.03 Co N6 B:Nco101 2.02 Co CO B:Nco101 0.00 Co N3 B:Nco101 1.98 Co N2 B:Nco101 2.00 Co N5 B:Nco101 1.95 Co N4 B:Nco101 1.96 interactive model: Cobalt binding site 2 out of 2 in 3b5f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 3b5f. 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: B: G11, B: G12, B: G13, B: Nco102, conact list: Atom Atom Distance (A) Co N7 B:G11 4.57 Co O6 B:G11 4.78 Co C6 B:G12 4.96 Co N7 B:G12 4.40 Co O6 B:G12 4.14 Co O6 B:G13 4.60 Co N1 B:Nco102 2.04 Co N6 B:Nco102 2.01 Co CO B:Nco102 0.00 Co N3 B:Nco102 2.00 Co N2 B:Nco102 2.01 Co N5 B:Nco102 1.96 Co N4 B:Nco102 1.97 interactive model: