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

The structure of Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate'), PDB code: 3i1d was solved by D.R.Boer, I.Uson, M.J.Hannon, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.18 / 2.50
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	74.970, 74.970, 74.970, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 25.9

The binding sites of Iron atom in the 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 within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate'), PDB code: 3i1d:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate')


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate') within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:42.2 occ:0.33 N14 A:NPM203 2.0 42.6 0.3 N13 A:NPM204 2.0 39.9 0.3 N13 A:NPM205 2.0 40.6 0.3 N14 A:NPM205 2.0 46.4 0.3 N13 A:NPM203 2.0 38.1 0.3 N14 A:NPM204 2.0 45.7 0.3 C1T A:NPM205 2.6 43.9 0.3 C1U A:NPM205 2.7 46.0 0.3 C1T A:NPM203 2.7 40.4 0.3 C1U A:NPM203 2.8 42.3 0.3 C1T A:NPM204 2.8 43.5 0.3 C1U A:NPM204 2.9 46.0 0.3 C1Y A:NPM203 3.0 44.2 0.3 C1Y A:NPM204 3.1 46.3 0.3 C1Y A:NPM205 3.1 48.6 0.3 C1Q A:NPM204 3.1 36.8 0.3 C1Q A:NPM203 3.2 35.7 0.3 C1Q A:NPM205 3.3 37.2 0.3 C1P A:NPM204 3.6 35.7 0.3 C1P A:NPM203 3.9 34.6 0.3 C1P A:NPM205 4.0 36.3 0.3 C1V A:NPM205 4.1 46.5 0.3 C1V A:NPM203 4.1 44.2 0.3 C1R A:NPM204 4.1 34.1 0.3 C1R A:NPM203 4.2 33.2 0.3 C1R A:NPM205 4.2 35.4 0.3 C1X A:NPM203 4.2 44.9 0.3 C1V A:NPM204 4.3 45.4 0.3 C1X A:NPM204 4.3 45.4 0.3 C1X A:NPM205 4.3 48.2 0.3 C1W A:NPM203 4.7 45.1 0.3 C1W A:NPM205 4.7 47.9 0.3 C1W A:NPM204 4.9 44.7 0.3 C1O A:NPM204 4.9 35.2 0.3

Iron binding site 2 out of 6 in the Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate')


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate') within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe102 b:46.9 occ:0.33 N12 A:NPM204 2.0 44.0 0.3 N11 A:NPM203 2.0 46.7 0.3 N12 A:NPM205 2.0 47.5 0.3 N11 A:NPM204 2.0 47.8 0.3 N11 A:NPM205 2.0 50.4 0.3 N12 A:NPM203 2.0 44.0 0.3 C1F A:NPM204 2.6 46.4 0.3 C1F A:NPM203 2.7 45.2 0.3 C1E A:NPM204 2.7 47.1 0.3 C1F A:NPM205 2.7 50.3 0.3 C1E A:NPM203 2.7 46.7 0.3 C1E A:NPM205 2.8 51.3 0.3 C1A A:NPM203 3.0 47.5 0.3 C1A A:NPM204 3.0 48.9 0.3 C1A A:NPM205 3.1 50.4 0.3 C1G A:NPM203 3.1 41.5 0.3 C1G A:NPM205 3.2 45.0 0.3 C1G A:NPM204 3.2 40.4 0.3 C1L A:NPM203 3.7 40.5 0.3 C1L A:NPM205 3.8 43.5 0.3 C1L A:NPM204 4.0 39.3 0.3 C1D A:NPM203 4.0 47.9 0.3 C1D A:NPM204 4.0 47.7 0.3 C1H A:NPM204 4.1 38.7 0.3 C1H A:NPM205 4.1 44.0 0.3 C1D A:NPM205 4.1 51.1 0.3 C1H A:NPM203 4.2 40.3 0.3 C1B A:NPM203 4.2 48.2 0.3 C1B A:NPM204 4.3 48.5 0.3 C1B A:NPM205 4.3 49.1 0.3 C1C A:NPM203 4.6 48.4 0.3 C1C A:NPM204 4.7 48.6 0.3 C1C A:NPM205 4.8 50.0 0.3

Iron binding site 3 out of 6 in the Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate')


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate') within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe7 b:51.4 occ:0.50 N13 B:NPM204 2.0 46.1 0.5 N14 B:NPM205 2.0 49.3 0.5 N14 B:NPM203 2.0 59.9 0.5 N14 B:NPM204 2.0 55.2 0.5 N13 B:NPM205 2.0 45.0 0.5 N13 B:NPM203 2.0 53.1 0.5 C1T B:NPM205 2.7 47.0 0.5 C1T B:NPM204 2.7 51.2 0.5 C1U B:NPM205 2.8 48.7 0.5 C1T B:NPM203 2.8 56.3 0.5 C1U B:NPM204 2.8 54.2 0.5 C1U B:NPM203 2.8 60.3 0.5 C1Y B:NPM205 3.0 50.5 0.5 C1Y B:NPM203 3.0 61.8 0.5 C1Q B:NPM204 3.0 41.7 0.5 C1Y B:NPM204 3.1 55.2 0.5 C1Q B:NPM203 3.1 51.1 0.5 C1Q B:NPM205 3.2 40.5 0.5 C1P B:NPM204 3.6 40.2 0.5 C1P B:NPM203 3.8 49.0 0.5 C1P B:NPM205 3.9 39.6 0.5 C1R B:NPM204 4.0 38.8 0.5 C1R B:NPM203 4.1 49.2 0.5 C1R B:NPM205 4.1 39.1 0.5 C1V B:NPM205 4.1 49.9 0.5 C1V B:NPM204 4.2 54.7 0.5 C1V B:NPM203 4.2 62.0 0.5 C1X B:NPM205 4.2 50.4 0.5 C1X B:NPM203 4.3 62.2 0.5 C1X B:NPM204 4.3 55.5 0.5 C1W B:NPM205 4.7 50.9 0.5 C1W B:NPM204 4.8 55.1 0.5 C1W B:NPM203 4.8 62.9 0.5 C1O B:NPM204 4.9 39.0 0.5

Iron binding site 4 out of 6 in the Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate')


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate') within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe102 b:54.4 occ:0.50 N12 B:NPM204 2.0 51.5 0.5 N11 B:NPM203 2.0 56.0 0.5 N11 B:NPM205 2.0 58.5 0.5 N12 B:NPM205 2.0 51.2 0.5 N12 B:NPM203 2.0 52.0 0.5 N11 B:NPM204 2.0 60.6 0.5 C1F B:NPM203 2.7 53.8 0.5 C1F B:NPM205 2.7 54.5 0.5 C1E B:NPM203 2.7 56.3 0.5 C1F B:NPM204 2.7 56.6 0.5 C1E B:NPM205 2.8 57.8 0.5 C1E B:NPM204 2.8 60.2 0.5 C1A B:NPM205 3.0 60.5 0.5 C1A B:NPM203 3.0 56.8 0.5 C1A B:NPM204 3.1 62.0 0.5 C1G B:NPM205 3.1 47.1 0.5 C1G B:NPM204 3.2 46.6 0.5 C1G B:NPM203 3.2 49.6 0.5 C1L B:NPM203 3.8 49.5 0.5 C1L B:NPM204 3.8 43.2 0.5 C1L B:NPM205 3.9 47.2 0.5 C1H B:NPM205 4.0 43.7 0.5 C1D B:NPM203 4.1 56.9 0.5 C1D B:NPM205 4.1 59.3 0.5 C1H B:NPM204 4.1 44.0 0.5 C1D B:NPM204 4.2 60.7 0.5 C1H B:NPM203 4.2 47.5 0.5 C1B B:NPM205 4.3 60.8 0.5 C1B B:NPM203 4.3 56.9 0.5 C2' B:DG6 4.3 45.4 0.5 C1B B:NPM204 4.3 62.2 0.5 O3' B:DG6 4.4 50.0 0.5 C1C B:NPM205 4.7 60.4 0.5 C1C B:NPM203 4.7 56.5 0.5 C1C B:NPM204 4.8 61.7 0.5 C1' B:DG6 4.9 42.9 0.5 C3' B:DG6 4.9 47.7 0.5

Iron binding site 5 out of 6 in the Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate')


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate') within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:0.9 occ:0.17 N13 B:NPM10 2.0 0.1 0.2 N13 B:NPM9 2.0 0.1 0.2 N13 B:NPM8 2.0 1.0 0.2 N14 B:NPM10 2.0 0.3 0.2 N14 B:NPM8 2.0 0.8 0.2 N14 B:NPM9 2.0 0.7 0.2 C1T B:NPM8 2.7 0.5 0.2 C1T B:NPM10 2.8 0.4 0.2 C1T B:NPM9 2.8 0.4 0.2 C1U B:NPM8 2.8 0.6 0.2 C1U B:NPM10 2.8 0.3 0.2 C1U B:NPM9 2.8 0.4 0.2 C1Y B:NPM10 3.0 0.8 0.2 C1Y B:NPM9 3.0 0.8 0.2 C1Y B:NPM8 3.0 0.3 0.2 C1Q B:NPM9 3.2 97.8 0.2 C1Q B:NPM10 3.2 0.5 0.2 C1Q B:NPM8 3.2 98.9 0.2 C1P B:NPM9 3.8 97.0 0.2 C1P B:NPM8 3.9 98.2 0.2 C1P B:NPM10 3.9 100.0 0.2 C1R B:NPM10 4.0 99.8 0.2 C1R B:NPM8 4.1 98.0 0.2 C1R B:NPM9 4.1 96.9 0.2 C1V B:NPM8 4.2 0.0 0.2 C1V B:NPM10 4.2 0.9 0.2 C1V B:NPM9 4.2 0.8 0.2 C1X B:NPM10 4.3 0.1 0.2 C1X B:NPM8 4.3 0.5 0.2 C1X B:NPM9 4.3 1.0 0.2 C1W B:NPM8 4.8 0.4 0.2 C1W B:NPM10 4.8 0.1 0.2 C1W B:NPM9 4.8 1.0 0.2

Iron binding site 6 out of 6 in the Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate')


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Distinct Recognition of Three-Way Dna Junctions By the Two Enantiomers of A Metallo-Supramolecular Cylinder ('Helicate') within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe7 b:96.3 occ:0.17 N12 B:NPM8 2.0 95.7 0.2 N12 B:NPM10 2.0 97.4 0.2 N11 B:NPM10 2.0 98.6 0.2 N11 B:NPM9 2.0 97.1 0.2 N12 B:NPM9 2.0 95.2 0.2 N11 B:NPM8 2.0 96.0 0.2 C1F B:NPM9 2.8 96.0 0.2 C1F B:NPM10 2.8 98.4 0.2 C1F B:NPM8 2.8 96.0 0.2 C1E B:NPM9 2.8 96.9 0.2 C1E B:NPM10 2.9 98.8 0.2 C1E B:NPM8 2.9 96.0 0.2 C1A B:NPM10 3.0 99.3 0.2 C1A B:NPM9 3.0 97.3 0.2 C1A B:NPM8 3.0 95.9 0.2 C1G B:NPM8 3.1 95.1 0.2 C1G B:NPM9 3.2 94.4 0.2 C1G B:NPM10 3.2 97.3 0.2 C1L B:NPM8 3.7 95.0 0.2 C1L B:NPM9 3.9 94.0 0.2 C1L B:NPM10 3.9 97.1 0.2 C1H B:NPM9 4.1 94.1 0.2 C1H B:NPM8 4.1 95.0 0.2 C1H B:NPM10 4.1 97.2 0.2 C1D B:NPM9 4.2 97.2 0.2 C1D B:NPM10 4.2 99.0 0.2 C1D B:NPM8 4.2 96.1 0.2 C1B B:NPM10 4.3 99.5 0.2 C1B B:NPM9 4.3 97.3 0.2 C1B B:NPM8 4.3 96.0 0.2 C1C B:NPM9 4.8 97.5 0.2 C1C B:NPM10 4.8 99.3 0.2 C1C B:NPM8 4.8 96.1 0.2 C1K B:NPM8 5.0 95.0 0.2

D.R.Boer, J.M.Kerckhoffs, Y.Parajo, M.Pascu, I.Uson, P.Lincoln, M.J.Hannon, M.Coll. Self-Assembly of Functionalizable Two-Component 3D Dna Arrays Through the Induced Formation of Dna Three-Way-Junction Branch Points By Supramolecular Cylinders. Angew.Chem.Int.Ed.Engl. V. 49 2336 2010.
ISSN: ISSN 1433-7851
PubMed: 20191645
DOI: 10.1002/ANIE.200906742