Magnesium in PDB 7jon: Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction

The structure of Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction, PDB code: 7jon was solved by C.R.Simmons, T.Macculloch, N.Stephanopoulos, H.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.31 / 3.11
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	68.625, 68.625, 55.959, 90, 90, 120
R / Rfree (%)	22.7 / 24.4

The structure of Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Magnesium atom in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction (pdb code 7jon). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction, PDB code: 7jon:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:43.2 occ:1.00 O6 A:DG3 3.0 68.5 1.0 C6 A:DG3 4.1 70.2 1.0 O6 D:DG15 4.3 86.8 1.0 H62 A:DA2 4.4 78.0 1.0 N7 A:DA2 4.5 75.7 1.0 H42 A:DC4 4.6 99.5 1.0 H41 A:DC4 4.7 99.5 1.0 N7 A:DG3 4.7 73.0 1.0 C5 A:DG3 4.8 71.3 1.0 N4 A:DC4 4.9 82.8 1.0 N6 A:DA2 4.9 64.8 1.0

Magnesium binding site 2 out of 3 in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:67.9 occ:1.00 N7 C:DA5 4.0 67.3 1.0 N7 C:DG6 4.2 51.9 1.0 O6 C:DG6 4.2 47.2 1.0 H8 C:DA5 4.3 84.6 1.0 C8 C:DA5 4.4 70.4 1.0 H62 C:DA5 4.9 65.0 1.0 C5 C:DA5 4.9 64.8 1.0 C6 C:DG6 4.9 52.9 1.0 C5 C:DG6 5.0 48.2 1.0

Magnesium binding site 3 out of 3 in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Self-Assembly of A 3D Dna Crystal Lattice (4X6 Duplex Version) Containing the J23 Immobile Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:55.5 occ:1.00 O2 C:DT3 2.6 70.0 1.0 H1' C:DT3 3.1 104.1 1.0 O4' C:DG4 3.5 84.3 1.0 H5' C:DG4 3.7 103.2 1.0 C2 C:DT3 3.7 68.9 1.0 H4' C:DG4 3.8 107.4 1.0 C1' C:DT3 3.9 86.6 1.0 H2 A:DA21 4.0 82.2 1.0 C4' C:DG4 4.1 89.4 1.0 O4' C:DT3 4.1 99.8 1.0 N1 C:DT3 4.4 67.6 1.0 C5' C:DG4 4.4 85.8 1.0 N3 C:DG4 4.7 63.7 1.0 C1' C:DG4 4.7 71.2 1.0 H1' C:DG4 4.8 85.6 1.0 H5'' C:DG4 4.8 103.2 1.0 N3 C:DT3 4.9 53.7 1.0 H3 C:DT3 4.9 64.6 1.0 C2 A:DA21 4.9 68.4 1.0

C.R.Simmons, T.Macculloch, N.Stephanopoulos, H.Yan. Structural and Computational Based Approach For the Creation of A Toolbox of Immobile Holliday Junctions For Dna-Directed Self-Assembly To Be Published.