Magnesium in PDB 6x8b: Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J6 Immobile Holliday Junction

The structure of Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J6 Immobile Holliday Junction, PDB code: 6x8b 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)	29.78 / 2.90
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	68.848, 68.848, 59.374, 90, 90, 120
R / Rfree (%)	23.8 / 25.1

The structure of Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J6 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 (4X5 Duplex Version) Containing the J6 Immobile Holliday Junction (pdb code 6x8b). 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 (4X5 Duplex Version) Containing the J6 Immobile Holliday Junction, PDB code: 6x8b:
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 (4X5 Duplex Version) Containing the J6 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 (4X5 Duplex Version) Containing the J6 Immobile Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:132.9 occ:1.00 N7 A:DG3 3.4 120.4 1.0 O6 A:DG3 3.9 143.8 1.0 N7 A:DA2 4.0 126.3 1.0 N4 A:DC4 4.1 139.5 1.0 C5 A:DG3 4.2 128.6 1.0 C8 A:DG3 4.4 118.2 1.0 C5 A:DA2 4.4 127.1 1.0 C6 A:DG3 4.4 138.6 1.0 O6 D:DG15 4.4 142.3 1.0 C8 A:DA2 4.5 126.7 1.0 C6 A:DA2 4.8 123.7 1.0 N6 A:DA2 4.8 123.8 1.0

Magnesium binding site 2 out of 3 in the Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J6 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 (4X5 Duplex Version) Containing the J6 Immobile Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:84.8 occ:1.00 O2 B:DT5 3.7 100.0 1.0 N2 A:DG11 4.2 96.1 1.0 C1' B:DT5 4.4 78.2 1.0 O4' B:DT5 4.6 90.4 1.0 O4' A:DA12 4.7 91.1 1.0 C2 B:DT5 4.7 80.8 1.0 N3 A:DG11 4.8 93.7 1.0 C2 A:DG11 5.0 87.4 1.0

Magnesium binding site 3 out of 3 in the Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J6 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 (4X5 Duplex Version) Containing the J6 Immobile Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:67.0 occ:1.00 OP2 C:DG8 2.6 94.5 1.0 P C:DG8 3.9 105.6 1.0 C8 C:DG8 4.0 57.7 1.0 O5' C:DG8 4.2 78.7 1.0 N7 C:DG8 4.3 61.8 1.0 N7 C:DA9 4.5 51.7 1.0 OP1 C:DG8 4.8 97.4 1.0 C8 C:DA9 4.9 56.4 1.0 O3' C:DT7 5.0 85.9 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.