Magnesium in PDB 6xo7: Self-Assembly of A 3D Dna Crystal Lattice (4X6 Junction Version) Containing the J30 Immobile Holliday Junction

The structure of Self-Assembly of A 3D Dna Crystal Lattice (4X6 Junction Version) Containing the J30 Immobile Holliday Junction, PDB code: 6xo7 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)	34.07 / 3.11
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	68.141, 68.141, 52.765, 90, 90, 120
R / Rfree (%)	21.5 / 24

The structure of Self-Assembly of A 3D Dna Crystal Lattice (4X6 Junction Version) Containing the J30 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 Junction Version) Containing the J30 Immobile Holliday Junction (pdb code 6xo7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Junction Version) Containing the J30 Immobile Holliday Junction, PDB code: 6xo7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Junction Version) Containing the J30 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 Junction Version) Containing the J30 Immobile Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg102 b:73.8 occ:1.00 N7 D:DA6 3.4 73.2 1.0 N7 D:DG7 3.5 59.8 1.0 O6 D:DG7 3.5 60.6 1.0 H8 D:DA6 3.5 89.0 1.0 C8 D:DA6 3.6 74.2 1.0 C5 D:DG7 4.2 59.8 1.0 C6 D:DG7 4.2 62.0 1.0 C5 D:DA6 4.3 70.9 1.0 H2' D:DA6 4.4 107.9 1.0 C8 D:DG7 4.6 62.8 1.0 N9 D:DA6 4.6 71.7 1.0 H62 D:DA6 4.7 89.7 1.0 H8 D:DG7 4.8 75.4 1.0 C4 D:DA6 5.0 74.0 1.0 H62 B:DA16 5.0 72.6 1.0

Magnesium binding site 2 out of 2 in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Junction Version) Containing the J30 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 Junction Version) Containing the J30 Immobile Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg103 b:87.4 occ:1.00 H21 D:DG11 2.5 105.3 1.0 N3 D:DG11 2.6 67.0 1.0 H1' D:DT12 2.7 107.6 1.0 H2'' D:DG11 2.8 99.2 1.0 N2 D:DG11 3.2 87.8 1.0 H1' D:DG11 3.3 89.5 1.0 C2 D:DG11 3.3 79.7 1.0 C2' D:DG11 3.5 82.7 1.0 C1' D:DT12 3.5 89.7 1.0 H2' D:DG11 3.5 99.2 1.0 O4' D:DT12 3.8 74.7 1.0 C4 D:DG11 3.8 63.3 1.0 C1' D:DG11 3.8 74.6 1.0 O2 A:DC9 3.8 85.7 1.0 H22 D:DG11 4.0 105.3 1.0 H4' D:DT12 4.0 108.0 1.0 H22 D:DG10 4.1 89.0 1.0 N1 D:DT12 4.1 89.7 1.0 H21 D:DG10 4.2 89.0 1.0 N9 D:DG11 4.2 58.8 1.0 H5' A:DT10 4.2 148.6 1.0 N2 D:DG10 4.3 74.2 1.0 C4' D:DT12 4.5 90.0 1.0 H1' A:DC9 4.5 127.1 1.0 H6 D:DT12 4.6 105.4 1.0 C6 D:DT12 4.6 87.9 1.0 H2'' D:DT12 4.6 110.2 1.0 C2 A:DC9 4.6 81.1 1.0 N1 D:DG11 4.7 76.0 1.0 C2 D:DT12 4.7 99.1 1.0 C2' D:DT12 4.7 91.8 1.0 O2 D:DT12 4.8 109.2 1.0 C3' D:DG11 4.9 93.6 1.0 O4' A:DT10 5.0 117.5 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.