Cobalt in the structure of Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'-Phosphodiester Linkage Within Active Site (pdb 3bbk)

The binding sites of Cobalt atom in the structure of Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'-Phosphodiester Linkage Within Active Site (pdb code 3bbk). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 3bbk 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) 30.0-2.8 Space group P6122 a (A) 93.520 b (A) 93.520 c (A) 133.970 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.5 Rfree (%) 22.1 Cobalt Binding Sites: Cobalt binding site 1 out of 3 in 3bbk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 3bbk. 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 4.09 Co C6 B:G21 4.89 Co C5 B:G21 4.93 Co N7 B:G21 4.18 Co O6 B:G21 4.12 Co OP1 C:A40 4.15 Co P C:A40 4.62 Co OP2 C:A40 4.19 Co OP2 C:U41 3.90 Co N1 B:Nco101 2.03 Co N6 B:Nco101 2.01 Co CO B:Nco101 0.00 Co N3 B:Nco101 2.00 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 3 in 3bbk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 3bbk. 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, A: So4104, B: Nco102, conact list: Atom Atom Distance (A) Co N7 B:G11 4.76 Co O6 B:G11 4.97 Co N7 B:G12 4.41 Co O6 B:G12 4.31 Co O6 B:G13 4.24 Co O1 A:So4104 4.87 Co O3 A:So4104 4.99 Co N1 B:Nco102 2.04 Co N6 B:Nco102 2.02 Co CO B:Nco102 0.00 Co N3 B:Nco102 2.01 Co N2 B:Nco102 2.01 Co N5 B:Nco102 1.95 Co N4 B:Nco102 1.97 interactive model: Cobalt binding site 3 out of 3 in 3bbk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 3bbk. 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: G6, B: A23, B: C25, C: G36, C: C38, C: Nco103, conact list: Atom Atom Distance (A) Co O6 A:G6 4.32 Co OP2 B:A23 4.29 Co N4 B:C25 4.80 Co C8 C:G36 4.98 Co C6 C:G36 4.76 Co C5 C:G36 4.68 Co N7 C:G36 4.16 Co O6 C:G36 4.33 Co O2' C:C38 4.20 Co N1 C:Nco103 2.04 Co N6 C:Nco103 2.03 Co CO C:Nco103 0.00 Co N3 C:Nco103 1.99 Co N2 C:Nco103 2.02 Co N5 C:Nco103 1.96 Co N4 C:Nco103 1.95 interactive model: