Cobalt in the structure of Crystal Structure of Rnase T in Complex With A Duplex Dna Product (Stem Loop Dna With 2 Nucleotide 3' Overhang) (pdb 3va3)

The binding sites of Cobalt atom in the structure of Crystal Structure of Rnase T in Complex With A Duplex Dna Product (Stem Loop Dna With 2 Nucleotide 3' Overhang) (pdb code 3va3). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 3va3 structure was solved by Y.-Y.HSIAO, H.S.YUAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.9-2.7 Space group P21212 a (A) 100.266 b (A) 112.684 c (A) 57.793 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 26.3 Rfree (%) 29 Cobalt Binding Sites: Cobalt binding site 1 out of 2 in 3va3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 3va3. 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: Leu36, A: Val62, A: Glu63, A: Phe65, A: Gly92, A: Ala132, A: Arg135, A: Hoh402, conact list: Atom Atom Distance (A) Co CB A:Leu36 4.65 Co CG1 A:Val62 4.31 Co O A:Glu63 4.72 Co N A:Phe65 4.57 Co CB A:Phe65 4.16 Co CD2 A:Phe65 4.34 Co CG A:Phe65 4.71 Co CA A:Phe65 4.81 Co N A:Gly92 3.90 Co C A:Gly92 4.60 Co CA A:Gly92 3.46 Co O A:Ala132 4.95 Co CB A:Ala132 4.57 Co CA A:Ala132 4.86 Co CD A:Arg135 4.78 Co CZ A:Arg135 4.48 Co NE A:Arg135 3.84 Co NH2 A:Arg135 4.20 Co O A:Hoh402 3.07 interactive model: Cobalt binding site 2 out of 2 in 3va3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 3va3. 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: Leu36, B: Val62, B: Glu63, B: Phe65, B: Gly92, B: Tyr93, B: Ala132, B: Arg135, conact list: Atom Atom Distance (A) Co CB B:Leu36 4.71 Co CG1 B:Val62 4.37 Co O B:Glu63 4.74 Co CB B:Phe65 4.47 Co CD2 B:Phe65 4.80 Co O B:Gly92 5.00 Co N B:Gly92 4.24 Co C B:Gly92 4.41 Co CA B:Gly92 3.53 Co N B:Tyr93 4.97 Co O B:Ala132 4.87 Co CB B:Ala132 4.37 Co CA B:Ala132 4.72 Co CB B:Arg135 4.91 Co CD B:Arg135 4.93 Co CZ B:Arg135 3.94 Co NE B:Arg135 3.68 Co NH2 B:Arg135 3.28 interactive model: