Cobalt in PDB 8ta9: Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION1) 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 (POSITION1) Within A Self-Assembled 3D Dna Lattice (4X6), PDB code: 8ta9 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)	41.52 / 2.80
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	68.395, 68.395, 58.132, 90, 90, 120
R / Rfree (%)	19.2 / 24.4

The binding sites of Cobalt atom in the Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION1) Within A Self-Assembled 3D Dna Lattice (4X6) (pdb code 8ta9). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION1) Within A Self-Assembled 3D Dna Lattice (4X6), PDB code: 8ta9:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION1) Within A Self-Assembled 3D Dna Lattice (4X6)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION1) Within A Self-Assembled 3D Dna Lattice (4X6) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:151.2 occ:1.00 O4' A:DG15 3.7 96.1 1.0 N3 A:DG14 3.8 65.0 1.0 N2 A:DG14 3.8 86.1 1.0 C4' A:DG15 4.2 85.3 1.0 C2 A:DG14 4.2 79.3 1.0 N2 B:DG2 4.2 73.7 1.0 C5' A:DG15 4.6 84.3 1.0 O4' A:DG14 4.6 88.6 1.0 N3 B:DG2 4.8 57.3 1.0 C1' A:DG15 4.9 82.5 1.0 C1' A:DG14 4.9 80.0 1.0 C2 B:DG2 4.9 63.4 1.0 C4 A:DG14 4.9 60.9 1.0

Cobalt binding site 2 out of 2 in the Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION1) Within A Self-Assembled 3D Dna Lattice (4X6)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION1) Within A Self-Assembled 3D Dna Lattice (4X6) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co102 b:121.2 occ:1.00 N7 D:DG10 2.5 48.7 1.0 C8 D:DG10 3.4 50.6 1.0 C5 D:DG10 3.5 46.0 1.0 O6 D:DG10 3.6 50.1 1.0 C6 D:DG10 3.9 52.6 1.0 O6 D:DG11 4.2 74.3 1.0 N7 B:DA5 4.4 59.6 1.0 N9 D:DG10 4.6 50.4 1.0 C4 D:DG10 4.7 51.0 1.0 OP2 D:DG10 4.8 58.6 1.0 C8 B:DA5 4.9 64.0 1.0 C5 B:DA5 4.9 53.7 1.0 N7 D:DG11 4.9 72.2 1.0 C6 D:DG11 5.0 63.3 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