Arsenic 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:

Magnesium

(Mg)

2 atoms

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

Arsenic binding site 1 out of 4 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 Arsenic with other atoms in the As 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:As101 b:185.1 occ:1.00 O2 C:DT3 3.8 97.8 1.0 C2 A:DA21 4.0 84.8 1.0 N3 A:DA21 4.2 85.9 1.0 N1 A:DA21 4.9 81.0 1.0 C2 C:DT3 5.0 98.7 1.0

Arsenic binding site 2 out of 4 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 Arsenic with other atoms in the As 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 A:As102 b:135.7 occ:1.00 O6 A:DG15 3.7 69.9 1.0 O6 A:DG14 3.8 69.7 1.0 N7 A:DG14 3.9 65.7 1.0 N4 B:DC0 4.2 56.8 1.0 C6 A:DG14 4.5 70.4 1.0 C5 A:DG14 4.6 69.5 1.0 C6 A:DG15 4.8 66.2 1.0 C5 A:DC13 4.9 68.8 1.0 C8 A:DG14 5.0 72.6 1.0

Arsenic binding site 3 out of 4 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 Arsenic with other atoms in the As binding site number 3 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:As103 b:205.6 occ:1.00 O6 A:DG3 2.8 102.2 1.0 O6 D:DG15 3.3 116.5 1.0 C6 A:DG3 3.8 99.3 1.0 N7 A:DG3 4.2 97.1 1.0 N4 D:DC16 4.2 109.4 1.0 N4 A:DC4 4.2 98.3 1.0 C6 D:DG15 4.3 118.4 1.0 N7 A:DA2 4.3 95.6 1.0 C5 A:DG3 4.4 101.1 1.0 N6 A:DA2 4.7 103.3 1.0 C5 A:DA2 4.8 97.1 1.0 N7 D:DG15 5.0 118.1 1.0 N1 A:DG3 5.0 97.8 1.0 C7 D:DT14 5.0 100.5 1.0 C6 A:DA2 5.0 101.7 1.0

Arsenic binding site 4 out of 4 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 Arsenic with other atoms in the As binding site number 4 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 D:As101 b:144.2 occ:1.00 N7 D:DG10 3.8 55.9 1.0 N7 D:DG11 4.1 59.8 1.0 OP2 D:DG10 4.3 56.2 1.0 O6 D:DG11 4.4 70.7 1.0 O6 D:DG10 4.5 65.8 1.0 C8 D:DG10 4.5 56.1 1.0 C5 D:DG10 4.5 54.1 1.0 C6 D:DG10 4.8 60.4 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