Cobalt in the structure of Molecular Recognition By the Vitamin B12 Rna Aptamer (pdb 1ddy)

The binding sites of Cobalt atom in the structure of Molecular Recognition By the Vitamin B12 Rna Aptamer (pdb code 1ddy). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 1ddy structure was solved by D.SUSSMAN, J.C.NIX, C.WILSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 12.0-3.0 Space group C2221 a (A) 91.330 b (A) 161.880 c (A) 100.960 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 24.6 Cobalt Binding Sites: Cobalt binding site 1 out of 4 in 1ddy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 1ddy. 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: B12101, A: Nme102, conact list: Atom Atom Distance (A) Co C9B A:B12101 3.26 Co C18 A:B12101 4.14 Co C11 A:B12101 2.90 Co C1 A:B12101 2.92 Co C8 A:B12101 4.22 Co C2 A:B12101 4.25 Co C4B A:B12101 3.90 Co C46 A:B12101 4.83 Co N22 A:B12101 1.93 Co C35 A:B12101 4.90 Co C17 A:B12101 4.24 Co N21 A:B12101 1.91 Co C12 A:B12101 4.27 Co C19 A:B12101 2.86 Co C41 A:B12101 4.94 Co CO A:B12101 0.00 Co N1B A:B12101 4.23 Co C15 A:B12101 3.39 Co C37 A:B12101 4.88 Co C8B A:B12101 4.39 Co C16 A:B12101 2.96 Co C6 A:B12101 3.00 Co C5 A:B12101 3.39 Co C4 A:B12101 2.96 Co C10 A:B12101 3.24 Co C13 A:B12101 4.32 Co C2B A:B12101 3.02 Co C20 A:B12101 3.58 Co C48 A:B12101 4.97 Co N3B A:B12101 2.07 Co C9 A:B12101 2.87 Co C54 A:B12101 4.95 Co C14 A:B12101 3.01 Co N24 A:B12101 1.88 Co N23 A:B12101 1.95 Co C7 A:B12101 4.29 Co C53 A:B12101 4.94 Co C3 A:B12101 4.27 Co C26 A:B12101 4.70 Co N A:Nme102 2.99 Co C A:Nme102 1.85 interactive model: Cobalt binding site 2 out of 4 in 1ddy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 1ddy. 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: C: B12301, C: Nme302, conact list: Atom Atom Distance (A) Co C9B C:B12301 3.19 Co C18 C:B12301 4.11 Co C11 C:B12301 2.91 Co C1 C:B12301 2.89 Co C8 C:B12301 4.20 Co C2 C:B12301 4.20 Co C4B C:B12301 3.84 Co C46 C:B12301 4.75 Co N22 C:B12301 1.93 Co C35 C:B12301 4.89 Co C17 C:B12301 4.24 Co N21 C:B12301 1.89 Co C12 C:B12301 4.26 Co C19 C:B12301 2.83 Co C41 C:B12301 4.85 Co CO C:B12301 0.00 Co N1B C:B12301 4.12 Co C15 C:B12301 3.41 Co C37 C:B12301 4.74 Co C8B C:B12301 4.30 Co C16 C:B12301 2.97 Co C6 C:B12301 2.99 Co C5 C:B12301 3.37 Co C4 C:B12301 2.93 Co C10 C:B12301 3.25 Co C13 C:B12301 4.31 Co C2B C:B12301 2.92 Co C20 C:B12301 3.58 Co C48 C:B12301 4.85 Co N3B C:B12301 2.01 Co C9 C:B12301 2.87 Co C54 C:B12301 4.96 Co C14 C:B12301 3.01 Co N24 C:B12301 1.88 Co N23 C:B12301 1.96 Co C7 C:B12301 4.25 Co C53 C:B12301 4.96 Co C3 C:B12301 4.23 Co C26 C:B12301 4.58 Co N C:Nme302 2.99 Co C C:Nme302 1.85 interactive model: Cobalt binding site 3 out of 4 in 1ddy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 1ddy. 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: E: B12501, E: Nme502, conact list: Atom Atom Distance (A) Co C9B E:B12501 3.18 Co C18 E:B12501 4.10 Co C11 E:B12501 2.91 Co C1 E:B12501 2.89 Co C8 E:B12501 4.21 Co C2 E:B12501 4.19 Co C4B E:B12501 3.81 Co C46 E:B12501 4.79 Co N22 E:B12501 1.93 Co C35 E:B12501 4.90 Co C17 E:B12501 4.24 Co N21 E:B12501 1.89 Co C12 E:B12501 4.27 Co C19 E:B12501 2.84 Co C41 E:B12501 4.92 Co CO E:B12501 0.00 Co N1B E:B12501 4.17 Co C15 E:B12501 3.42 Co C37 E:B12501 4.84 Co C8B E:B12501 4.31 Co C16 E:B12501 2.98 Co C6 E:B12501 3.00 Co C5 E:B12501 3.37 Co C4 E:B12501 2.93 Co C10 E:B12501 3.24 Co C13 E:B12501 4.34 Co C2B E:B12501 2.96 Co C20 E:B12501 3.57 Co N3B E:B12501 2.03 Co C9 E:B12501 2.87 Co C54 E:B12501 4.95 Co C14 E:B12501 3.03 Co N24 E:B12501 1.88 Co N23 E:B12501 1.96 Co C7 E:B12501 4.29 Co C53 E:B12501 4.97 Co C3 E:B12501 4.23 Co C26 E:B12501 4.56 Co N E:Nme502 3.00 Co C E:Nme502 1.85 interactive model: Cobalt binding site 4 out of 4 in 1ddy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 1ddy. 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: G: B12701, G: Nme702, conact list: Atom Atom Distance (A) Co C9B G:B12701 3.24 Co C18 G:B12701 4.14 Co C11 G:B12701 2.91 Co C1 G:B12701 2.89 Co C8 G:B12701 4.20 Co C2 G:B12701 4.20 Co C4B G:B12701 3.91 Co C46 G:B12701 4.77 Co N22 G:B12701 1.93 Co C35 G:B12701 4.90 Co C17 G:B12701 4.28 Co N21 G:B12701 1.89 Co C12 G:B12701 4.25 Co C19 G:B12701 2.86 Co C41 G:B12701 4.88 Co CO G:B12701 0.00 Co N1B G:B12701 4.17 Co C15 G:B12701 3.43 Co C37 G:B12701 4.83 Co C8B G:B12701 4.34 Co C16 G:B12701 3.00 Co C6 G:B12701 3.00 Co C5 G:B12701 3.37 Co C4 G:B12701 2.93 Co C10 G:B12701 3.24 Co C13 G:B12701 4.32 Co C2B G:B12701 2.96 Co C20 G:B12701 3.55 Co C48 G:B12701 4.96 Co N3B G:B12701 2.04 Co C9 G:B12701 2.86 Co C54 G:B12701 4.99 Co C14 G:B12701 3.02 Co N24 G:B12701 1.90 Co N23 G:B12701 1.96 Co C7 G:B12701 4.27 Co C53 G:B12701 4.98 Co C3 G:B12701 4.22 Co C26 G:B12701 4.64 Co N G:Nme702 3.00 Co C G:Nme702 1.85 interactive model: