Magnesium in PDB 8tdt: Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X6)

The structure of Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X6), PDB code: 8tdt 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)	41.00 / 3.01
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	68.487, 68.487, 56.749, 90, 90, 120
R / Rfree (%)	19.9 / 23.1

The structure of Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X6) also contains other interesting chemical elements:

Arsenic

(As)

4 atoms

The binding sites of Magnesium atom in the Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X6) (pdb code 8tdt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X6), PDB code: 8tdt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X6) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:75.1 occ:1.00 O4' A:DG11 2.8 99.1 1.0 N3 A:DG11 3.0 72.8 1.0 O2 A:DT10 3.0 74.5 1.0 C2 A:DG11 3.7 70.4 1.0 C4 A:DG11 3.7 75.0 1.0 C4' A:DG11 3.7 98.1 1.0 C1' A:DG11 3.7 82.4 1.0 N2 A:DG11 3.8 76.4 1.0 N9 A:DG11 4.0 78.8 1.0 C2 A:DT10 4.1 73.8 1.0 C5' A:DG11 4.3 101.7 1.0 C1' A:DT10 4.7 82.3 1.0 N1 A:DG11 4.7 65.0 1.0 C2 B:DA5 4.7 62.0 1.0 C5 A:DG11 4.8 75.4 1.0 C3' A:DG11 4.9 87.0 1.0 N1 A:DT10 4.9 77.0 1.0 C2' A:DG11 5.0 82.3 1.0

Magnesium binding site 2 out of 2 in the Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X6) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:66.2 occ:1.00 O2 B:DT3 3.8 74.2 1.0 O2 A:DC13 3.9 72.9 1.0 O4' A:DG14 4.2 92.7 1.0 C5' B:DC4 4.6 82.0 1.0 N2 B:DG2 4.7 73.5 1.0 O4' B:DC4 4.7 76.5 1.0 C4' A:DG14 4.8 91.8 1.0 C1' A:DC13 4.9 71.8 1.0 C4' B:DC4 4.9 74.1 1.0 C2 B:DT3 4.9 71.6 1.0 C5' A:DG14 5.0 82.1 1.0

C.R.Simmons, A.Buchberger, S.J.W.Henry, A.Novacek, N.E.Fahmi, T.Macculloch, N.Stephanopoulos, H.Yan. Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional Dna Crystals. J.Am.Chem.Soc. V. 145 26075 2023.
ISSN: ESSN 1520-5126
PubMed: 37987645
DOI: 10.1021/JACS.3C07802