Iron in the structure of Distinct Recognition Of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate') (pdb 3i1d)

The binding sites of Iron atom in the structure of Distinct Recognition Of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate') (pdb code 3i1d). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3i1d structure was solved by D.R.BOER, I.USON, M.J.HANNON, M.COLL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 18.2-2.5 Space group P4332 a (A) 74.970 b (A) 74.970 c (A) 74.970 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.5 Rfree (%) 25.9 Iron Binding Sites: Iron binding site 1 out of 6 in 3i1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3i1d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Npm203, A: Npm204, A: Npm205, conact list: Atom Atom Distance (A) Fe C1X A:Npm203 4.23 Fe C1V A:Npm203 4.11 Fe C1Y A:Npm203 2.97 Fe C1U A:Npm203 2.77 Fe C1P A:Npm203 3.87 Fe C1R A:Npm203 4.17 Fe N13 A:Npm203 2.01 Fe N14 A:Npm203 1.97 Fe C1T A:Npm203 2.73 Fe C1W A:Npm203 4.70 Fe C1Q A:Npm203 3.21 Fe C1X A:Npm204 4.34 Fe C1V A:Npm204 4.26 Fe C1Y A:Npm204 3.06 Fe C1U A:Npm204 2.88 Fe C1P A:Npm204 3.61 Fe C1R A:Npm204 4.14 Fe N13 A:Npm204 1.98 Fe N14 A:Npm204 2.01 Fe C1O A:Npm204 4.93 Fe C1T A:Npm204 2.79 Fe C1W A:Npm204 4.86 Fe C1Q A:Npm204 3.11 Fe C1X A:Npm205 4.34 Fe C1V A:Npm205 4.07 Fe C1Y A:Npm205 3.10 Fe C1U A:Npm205 2.70 Fe C1P A:Npm205 3.96 Fe C1R A:Npm205 4.21 Fe N13 A:Npm205 1.99 Fe N14 A:Npm205 1.99 Fe C1T A:Npm205 2.60 Fe C1W A:Npm205 4.75 Fe C1Q A:Npm205 3.27 interactive model: Iron binding site 2 out of 6 in 3i1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3i1d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Npm203, A: Npm204, A: Npm205, conact list: Atom Atom Distance (A) Fe C1G A:Npm203 3.14 Fe C1L A:Npm203 3.72 Fe N12 A:Npm203 2.01 Fe C1B A:Npm203 4.21 Fe C1D A:Npm203 4.03 Fe C1E A:Npm203 2.74 Fe C1F A:Npm203 2.71 Fe N11 A:Npm203 1.99 Fe C1H A:Npm203 4.15 Fe C1A A:Npm203 2.97 Fe C1C A:Npm203 4.63 Fe C1G A:Npm204 3.23 Fe C1L A:Npm204 4.00 Fe N12 A:Npm204 1.97 Fe C1B A:Npm204 4.29 Fe C1D A:Npm204 4.04 Fe C1E A:Npm204 2.71 Fe C1F A:Npm204 2.62 Fe N11 A:Npm204 1.99 Fe C1H A:Npm204 4.09 Fe C1A A:Npm204 3.05 Fe C1C A:Npm204 4.69 Fe C1G A:Npm205 3.17 Fe C1L A:Npm205 3.83 Fe N12 A:Npm205 1.99 Fe C1B A:Npm205 4.35 Fe C1D A:Npm205 4.15 Fe C1E A:Npm205 2.80 Fe C1F A:Npm205 2.72 Fe N11 A:Npm205 2.01 Fe C1H A:Npm205 4.10 Fe C1A A:Npm205 3.07 Fe C1C A:Npm205 4.77 interactive model: Iron binding site 3 out of 6 in 3i1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3i1d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Npm203, B: Npm204, B: Npm205, conact list: Atom Atom Distance (A) Fe C1X B:Npm203 4.29 Fe C1V B:Npm203 4.19 Fe C1Y B:Npm203 3.01 Fe C1U B:Npm203 2.82 Fe C1P B:Npm203 3.77 Fe C1R B:Npm203 4.05 Fe N13 B:Npm203 2.01 Fe N14 B:Npm203 1.99 Fe C1T B:Npm203 2.78 Fe C1W B:Npm203 4.79 Fe C1Q B:Npm203 3.13 Fe C1X B:Npm204 4.31 Fe C1V B:Npm204 4.17 Fe C1Y B:Npm204 3.06 Fe C1U B:Npm204 2.80 Fe C1P B:Npm204 3.59 Fe C1R B:Npm204 3.98 Fe N13 B:Npm204 1.96 Fe N14 B:Npm204 2.00 Fe C1O B:Npm204 4.85 Fe C1T B:Npm204 2.72 Fe C1W B:Npm204 4.79 Fe C1Q B:Npm204 3.04 Fe C1X B:Npm205 4.23 Fe C1V B:Npm205 4.11 Fe C1Y B:Npm205 2.97 Fe C1U B:Npm205 2.75 Fe C1P B:Npm205 3.86 Fe C1R B:Npm205 4.08 Fe N13 B:Npm205 2.00 Fe N14 B:Npm205 1.96 Fe C1T B:Npm205 2.70 Fe C1W B:Npm205 4.69 Fe C1Q B:Npm205 3.19 interactive model: Iron binding site 4 out of 6 in 3i1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3i1d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Dg6, B: Npm203, B: Npm204, B: Npm205, conact list: Atom Atom Distance (A) Fe C3' B:Dg6 4.92 Fe C1' B:Dg6 4.88 Fe O3' B:Dg6 4.36 Fe C2' B:Dg6 4.31 Fe C1G B:Npm203 3.20 Fe C1L B:Npm203 3.76 Fe N12 B:Npm203 2.00 Fe C1B B:Npm203 4.30 Fe C1D B:Npm203 4.08 Fe C1E B:Npm203 2.74 Fe C1F B:Npm203 2.68 Fe N11 B:Npm203 1.98 Fe C1H B:Npm203 4.25 Fe C1A B:Npm203 3.04 Fe C1C B:Npm203 4.72 Fe C1G B:Npm204 3.17 Fe C1L B:Npm204 3.79 Fe N12 B:Npm204 1.98 Fe C1B B:Npm204 4.34 Fe C1D B:Npm204 4.20 Fe C1E B:Npm204 2.84 Fe C1F B:Npm204 2.75 Fe N11 B:Npm204 2.01 Fe C1H B:Npm204 4.15 Fe C1A B:Npm204 3.06 Fe C1C B:Npm204 4.81 Fe C1G B:Npm205 3.14 Fe C1L B:Npm205 3.87 Fe N12 B:Npm205 1.99 Fe C1B B:Npm205 4.29 Fe C1D B:Npm205 4.09 Fe C1E B:Npm205 2.76 Fe C1F B:Npm205 2.71 Fe N11 B:Npm205 1.99 Fe C1H B:Npm205 4.01 Fe C1A B:Npm205 3.02 Fe C1C B:Npm205 4.72 interactive model: Iron binding site 5 out of 6 in 3i1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3i1d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Npm9, B: Npm10, B: Npm8, conact list: Atom Atom Distance (A) Fe C1X B:Npm9 4.30 Fe C1V B:Npm9 4.21 Fe C1Y B:Npm9 3.02 Fe C1U B:Npm9 2.84 Fe C1P B:Npm9 3.81 Fe C1R B:Npm9 4.09 Fe N13 B:Npm9 2.00 Fe N14 B:Npm9 2.00 Fe C1T B:Npm9 2.77 Fe C1W B:Npm9 4.80 Fe C1Q B:Npm9 3.17 Fe C1X B:Npm10 4.29 Fe C1V B:Npm10 4.20 Fe C1Y B:Npm10 3.02 Fe C1U B:Npm10 2.84 Fe C1P B:Npm10 3.92 Fe C1R B:Npm10 4.00 Fe N13 B:Npm10 2.00 Fe N14 B:Npm10 2.00 Fe C1T B:Npm10 2.77 Fe C1W B:Npm10 4.79 Fe C1Q B:Npm10 3.17 Fe C1X B:Npm8 4.30 Fe C1V B:Npm8 4.19 Fe C1Y B:Npm8 3.03 Fe C1U B:Npm8 2.82 Fe C1P B:Npm8 3.91 Fe C1R B:Npm8 4.08 Fe N13 B:Npm8 2.00 Fe N14 B:Npm8 2.00 Fe C1T B:Npm8 2.75 Fe C1W B:Npm8 4.79 Fe C1Q B:Npm8 3.20 interactive model: Iron binding site 6 out of 6 in 3i1d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3i1d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Npm9, B: Npm10, B: Npm8, conact list: Atom Atom Distance (A) Fe C1G B:Npm9 3.18 Fe C1L B:Npm9 3.93 Fe N12 B:Npm9 2.01 Fe C1B B:Npm9 4.30 Fe C1D B:Npm9 4.16 Fe C1E B:Npm9 2.83 Fe C1F B:Npm9 2.77 Fe N11 B:Npm9 2.00 Fe C1H B:Npm9 4.06 Fe C1A B:Npm9 3.01 Fe C1C B:Npm9 4.76 Fe C1G B:Npm10 3.21 Fe C1L B:Npm10 3.95 Fe N12 B:Npm10 2.00 Fe C1B B:Npm10 4.30 Fe C1D B:Npm10 4.20 Fe C1E B:Npm10 2.86 Fe C1F B:Npm10 2.78 Fe N11 B:Npm10 2.00 Fe C1H B:Npm10 4.10 Fe C1A B:Npm10 3.00 Fe C1C B:Npm10 4.78 Fe C1G B:Npm8 3.11 Fe C1L B:Npm8 3.71 Fe N12 B:Npm8 2.00 Fe C1K B:Npm8 4.99 Fe C1B B:Npm8 4.31 Fe C1D B:Npm8 4.20 Fe C1E B:Npm8 2.86 Fe C1F B:Npm8 2.80 Fe N11 B:Npm8 2.01 Fe C1H B:Npm8 4.09 Fe C1A B:Npm8 3.02 Fe C1C B:Npm8 4.79 interactive model: