Magnesium in PDB 8tbd: Sequence Specific (Aatt) Orientation of Hoechst Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X5)

The structure of Sequence Specific (Aatt) Orientation of Hoechst Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X5), PDB code: 8tbd 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)	41.57 / 3.00
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	68.345, 68.345, 58.4, 90, 90, 120
R / Rfree (%)	24.5 / 27.1

The structure of Sequence Specific (Aatt) Orientation of Hoechst Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X5) also contains other interesting chemical elements:

Arsenic

(As)

4 atoms

The binding sites of Magnesium atom in the Sequence Specific (Aatt) Orientation of Hoechst Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X5) (pdb code 8tbd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Sequence Specific (Aatt) Orientation of Hoechst Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X5), PDB code: 8tbd:

Magnesium binding site 1 out of 1 in the Sequence Specific (Aatt) Orientation of Hoechst Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X5)


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 Hoechst Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:72.0 occ:1.00 O2 B:DT3 2.8 76.9 1.0 O4' B:DC4 3.1 73.0 1.0 O2 A:DC13 3.5 84.0 1.0 C4' B:DC4 3.8 73.4 1.0 C2 B:DT3 4.0 77.5 1.0 O4' A:DG14 4.1 87.1 1.0 C2 A:DA12 4.1 82.9 1.0 C5' B:DC4 4.2 72.4 1.0 C1' B:DC4 4.3 68.7 1.0 N2 B:DG2 4.3 83.2 1.0 C2 A:DC13 4.5 81.1 1.0 C4' A:DG14 4.5 86.3 1.0 C5' A:DG14 4.6 83.0 1.0 N1 B:DC4 4.6 68.5 1.0 C1' A:DC13 4.6 76.7 1.0 O4' A:DC13 4.6 81.9 1.0 C1' B:DT3 4.7 77.1 1.0 N3 A:DA12 4.7 81.8 1.0 O2 B:DC4 4.8 75.8 1.0 C2 B:DC4 4.8 72.9 1.0 N1 B:DT3 4.8 75.4 1.0 N3 B:DT3 4.9 78.7 1.0 N1 A:DA12 4.9 81.0 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