Arsenic 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:

Magnesium

(Mg)

1 atom

The binding sites of Arsenic 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 Arsenic atom.
In total 4 binding sites of Arsenic where 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:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 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 Arsenic with other atoms in the As 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 A:As101 b:206.6 occ:1.00 O6 A:DG3 3.4 123.4 1.0 O6 D:DG15 3.7 127.0 1.0 C7 D:DT14 4.0 111.7 1.0 C6 A:DG3 4.4 121.3 1.0 N4 D:DC16 4.7 124.1 1.0 C6 D:DG15 4.8 128.4 1.0 C5 D:DT14 4.8 117.4 1.0 N4 A:DC4 4.8 121.1 1.0 N7 D:DG15 4.8 123.3 1.0 O4 D:DT14 4.9 115.8 1.0 N7 A:DG3 5.0 119.1 1.0

Arsenic binding site 2 out of 4 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 Arsenic with other atoms in the As binding site number 2 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:As101 b:230.3 occ:1.00 O4 B:DT3 4.8 85.4 1.0

Arsenic binding site 3 out of 4 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 Arsenic with other atoms in the As binding site number 3 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:As102 b:266.9 occ:1.00 N7 B:DA5 4.6 68.9 1.0

Arsenic binding site 4 out of 4 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 Arsenic with other atoms in the As binding site number 4 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 C:As102 b:154.0 occ:1.00 OP1 C:DT9 4.3 59.4 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