Cobalt in the structure of Crystal Structure Of A Group I Ribozyme Domain: Principles of Rna Packing (pdb 1gid)

The binding sites of Cobalt atom in the structure of Crystal Structure Of A Group I Ribozyme Domain: Principles of Rna Packing (pdb code 1gid). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 1gid structure was solved by J.H.CATE, A.R.GOODING, E.PODELL, K.ZHOU, B.L.GOLDEN, C.E.KUNDROT, T.R.CECH, J.A.DOUDNA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.5 Space group P212121 a (A) 74.800 b (A) 128.700 c (A) 145.900 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.2 Rfree (%) 28.5 Cobalt Binding Sites: Cobalt binding site 1 out of 4 in 1gid Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 1gid. 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: G147, A: G148, A: G149, A: U155, A: Nco261, conact list: Atom Atom Distance (A) Co C6 A:G147 4.96 Co N7 A:G147 4.45 Co O6 A:G147 4.33 Co C6 A:G148 4.93 Co N7 A:G148 4.77 Co O6 A:G148 3.97 Co O6 A:G149 4.64 Co O4 A:U155 4.18 Co N1 A:Nco261 1.96 Co N6 A:Nco261 1.96 Co CO A:Nco261 0.00 Co N3 A:Nco261 1.96 Co N2 A:Nco261 1.96 Co N5 A:Nco261 1.96 Co N4 A:Nco261 1.96 interactive model: Cobalt binding site 2 out of 4 in 1gid Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 1gid. 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: G174, A: G175, A: G176, A: U177, A: Nco262, conact list: Atom Atom Distance (A) Co OP2 A:G174 3.82 Co N7 A:G175 4.53 Co OP2 A:G175 4.65 Co C6 A:G176 4.64 Co C5 A:G176 4.86 Co N7 A:G176 4.29 Co O6 A:G176 3.76 Co C4 A:U177 4.91 Co O4 A:U177 3.99 Co N1 A:Nco262 1.96 Co N6 A:Nco262 1.96 Co CO A:Nco262 0.00 Co N3 A:Nco262 1.96 Co N2 A:Nco262 1.96 Co N5 A:Nco262 1.96 Co N4 A:Nco262 1.96 interactive model: Cobalt binding site 3 out of 4 in 1gid Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 1gid. 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: G147, B: G148, B: G149, B: U155, B: Nco263, conact list: Atom Atom Distance (A) Co C6 B:G147 4.96 Co N7 B:G147 4.43 Co O6 B:G147 4.34 Co C6 B:G148 4.96 Co N7 B:G148 4.75 Co O6 B:G148 4.01 Co O6 B:G149 4.42 Co O4 B:U155 4.18 Co N1 B:Nco263 1.96 Co N6 B:Nco263 1.96 Co CO B:Nco263 0.00 Co N3 B:Nco263 1.96 Co N2 B:Nco263 1.96 Co N5 B:Nco263 1.96 Co N4 B:Nco263 1.96 interactive model: Cobalt binding site 4 out of 4 in 1gid Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 1gid. 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: G174, B: G175, B: G176, B: U177, B: Nco264, conact list: Atom Atom Distance (A) Co OP2 B:G174 3.86 Co N7 B:G175 4.50 Co OP2 B:G175 4.71 Co C6 B:G176 4.64 Co C5 B:G176 4.86 Co N7 B:G176 4.29 Co O6 B:G176 3.75 Co C4 B:U177 4.88 Co O4 B:U177 3.94 Co N1 B:Nco264 1.96 Co N6 B:Nco264 1.96 Co CO B:Nco264 0.00 Co N3 B:Nco264 1.97 Co N2 B:Nco264 1.96 Co N5 B:Nco264 1.96 Co N4 B:Nco264 1.96 interactive model: