Cobalt in the structure of The Structural Basis of Hammerhead Ribozyme Self-Cleavage (pdb 379d)

The binding sites of Cobalt atom in the structure of The Structural Basis of Hammerhead Ribozyme Self-Cleavage (pdb code 379d). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 379d structure was solved by J.B.MURRAY, D.P.TERWEY, L.MALONEY, A.KARPEISKY, N.USMAN, L.BEIGELMAN, W.G.SCOTT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-3.1 Space group P3121 a (A) 65.100 b (A) 65.100 c (A) 138.700 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23 Rfree (%) n/a Cobalt Binding Sites: Cobalt binding site 1 out of 8 in 379d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 379d. 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: G23, A: G22, conact list: Atom Atom Distance (A) Co O6 A:G23 4.43 Co C6 A:G22 4.75 Co C5 A:G22 4.78 Co N7 A:G22 4.06 Co O6 A:G22 4.01 interactive model: Cobalt binding site 2 out of 8 in 379d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 379d. 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: U40, A: G50, A: A60, conact list: Atom Atom Distance (A) Co O2' A:U40 3.97 Co N9 A:G50 4.39 Co OP1 A:G50 4.25 Co C8 A:G50 3.28 Co C6 A:G50 3.44 Co N1 A:G50 4.81 Co C5 A:G50 3.09 Co N7 A:G50 2.21 Co C4 A:G50 4.32 Co O6 A:G50 3.13 Co N6 A:A60 4.26 interactive model: Cobalt binding site 3 out of 8 in 379d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 379d. 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: A34, B: G164, conact list: Atom Atom Distance (A) Co OP2 B:A34 3.98 Co N9 B:G164 4.51 Co C8 B:G164 3.60 Co C6 B:G164 2.73 Co N1 B:G164 4.09 Co C5 B:G164 2.78 Co N7 B:G164 2.36 Co C4 B:G164 4.12 Co OP2 B:G164 4.77 Co O6 B:G164 2.21 interactive model: Cobalt binding site 4 out of 8 in 379d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 379d. 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: G31, B: A34, B: G164, B: A163, conact list: Atom Atom Distance (A) Co N3 B:G31 4.69 Co N2 B:G31 4.17 Co C2 B:G31 4.77 Co C5 B:A34 4.95 Co N7 B:A34 4.56 Co N9 B:G164 3.04 Co N3 B:G164 2.17 Co N2 B:G164 3.66 Co C3' B:G164 4.02 Co C8 B:G164 4.39 Co C2 B:G164 3.27 Co C6 B:G164 4.96 Co N1 B:G164 4.48 Co C5 B:G164 4.23 Co C1' B:G164 2.59 Co N7 B:G164 4.99 Co O3' B:G164 4.85 Co O4' B:G164 3.94 Co C4 B:G164 2.89 Co C2' B:G164 2.55 Co C4' B:G164 4.64 Co O2' B:G164 2.78 Co N9 B:A163 3.58 Co C8 B:A163 3.49 Co C5 B:A163 4.54 Co C1' B:A163 3.76 Co N7 B:A163 4.11 Co O4' B:A163 3.51 Co C4 B:A163 4.27 Co C4' B:A163 4.91 Co O5' B:A163 4.95 interactive model: Cobalt binding site 5 out of 8 in 379d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 379d. 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: C170, B: A11, conact list: Atom Atom Distance (A) Co C3' B:C170 3.81 Co O3' B:C170 3.46 Co C5' B:C170 3.35 Co C4' B:C170 4.08 Co O5' B:C170 4.49 Co N9 B:A11 4.24 Co C8 B:A11 2.88 Co C6 B:A11 4.93 Co C5 B:A11 3.97 Co N6 B:A11 4.93 Co N7 B:A11 2.61 Co O4' B:A11 4.94 Co C4 B:A11 4.78 Co O5' B:A11 4.70 interactive model: Cobalt binding site 6 out of 8 in 379d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 379d. 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: G25, A: U24, conact list: Atom Atom Distance (A) Co N9 A:G25 4.16 Co C8 A:G25 3.11 Co C6 A:G25 3.03 Co N1 A:G25 4.42 Co C5 A:G25 2.73 Co N7 A:G25 1.94 Co C4 A:G25 4.00 Co O6 A:G25 2.72 Co O4 A:U24 4.51 interactive model: Cobalt binding site 7 out of 8 in 379d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 379d. 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: A163, B: G162, conact list: Atom Atom Distance (A) Co C5 B:A163 4.95 Co N7 B:A163 4.72 Co N9 B:G162 4.68 Co C8 B:G162 3.81 Co C6 B:G162 2.74 Co N1 B:G162 4.09 Co C5 B:G162 2.90 Co P B:G162 4.93 Co N7 B:G162 2.56 Co C4 B:G162 4.26 Co OP2 B:G162 3.53 Co O6 B:G162 2.09 interactive model: Cobalt binding site 8 out of 8 in 379d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 379d. 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: G80, A: A90, A: G101, A: G102, B: G120, conact list: Atom Atom Distance (A) Co O3' A:G80 4.95 Co C2' A:G80 4.48 Co O2' A:G80 3.83 Co OP1 A:A90 4.27 Co P A:A90 3.58 Co OP2 A:A90 2.49 Co C5' A:A90 4.60 Co O5' A:A90 3.64 Co N9 A:G101 4.12 Co N3 A:G101 4.88 Co C8 A:G101 3.21 Co C2 A:G101 4.87 Co C6 A:G101 2.54 Co N1 A:G101 3.94 Co C5 A:G101 2.45 Co N7 A:G101 1.95 Co C4 A:G101 3.78 Co OP2 A:G101 4.09 Co O6 A:G101 2.16 Co N7 A:G102 4.87 Co N2 B:G120 4.34 interactive model: