Magnesium in PDB 7jkk: Self-Assembly of A 3D Dna Crystal Lattice (4X6 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry

The structure of Self-Assembly of A 3D Dna Crystal Lattice (4X6 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry, PDB code: 7jkk 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)	46.02 / 2.79
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	113.078, 113.078, 52.131, 90, 90, 120
R / Rfree (%)	23 / 25.7

The structure of Self-Assembly of A 3D Dna Crystal Lattice (4X6 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Magnesium atom in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry (pdb code 7jkk). 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 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry, PDB code: 7jkk:
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 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry


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 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:77.0 occ:1.00 O4' B:DG17 3.7 90.8 1.0 N3 B:DG17 3.8 56.6 1.0 O2 B:DT16 4.3 71.3 1.0 C1' B:DG17 4.4 77.9 1.0 N2 B:DG17 4.4 56.0 1.0 C2 B:DG17 4.4 56.9 1.0 C4' B:DG17 4.6 93.2 1.0 C4 B:DG17 4.6 60.1 1.0 N3 A:DA6 4.8 63.8 1.0 N9 B:DG17 4.8 65.4 1.0 C2 A:DA6 4.8 67.3 1.0

Magnesium binding site 2 out of 3 in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry


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 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:100.3 occ:1.00 N3 C:DG30 4.0 81.2 1.0 N2 C:DG30 4.0 82.9 1.0 C2 C:DG30 4.4 80.8 1.0 O4' C:DG30 4.7 110.5 1.0 O4' C:DA31 4.8 103.3 1.0 C4 C:DG30 5.0 86.0 1.0

Magnesium binding site 3 out of 3 in the Self-Assembly of A 3D Dna Crystal Lattice (4X6 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry


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 Scramble Duplex Version) Containing the J10 Immobile Holliday Junction with R3 Symmetry within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:84.7 occ:1.00 N2 A:DG3 3.7 61.2 1.0 N2 B:DG20 3.8 57.6 1.0 N3 A:DG3 3.8 63.3 1.0 N3 B:DG20 3.9 57.2 1.0 O4' A:DT4 4.0 75.2 1.0 C2 A:DG3 4.2 60.8 1.0 C2 B:DG20 4.3 56.1 1.0 C4' A:DT4 4.5 73.1 1.0 O4' B:DT21 4.6 76.3 1.0 C5' A:DT4 4.8 76.2 1.0 C4' B:DT21 4.8 81.4 1.0 C4 A:DG3 4.9 60.2 1.0 C4 B:DG20 5.0 59.0 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.