Magnesium in PDB 8tb4: Sequence Specific (Aatt) Orientation of Dapi 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 Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X5), PDB code: 8tb4 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)	42.37 / 3.11
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	69.507, 69.507, 59.552, 90, 90, 120
R / Rfree (%)	19.5 / 23.8

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 (4X5) (pdb code 8tb4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 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 (4X5), PDB code: 8tb4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Sequence Specific (Aatt) Orientation of Dapi 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 Dapi 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:Mg102 b:127.2 occ:1.00 O6 A:DG11 4.2 121.7 1.0 N7 A:DG11 4.4 101.8 1.0 O4 B:DT3 4.6 116.6 1.0 N6 A:DA12 4.8 107.6 1.0 C6 A:DG11 5.0 102.0 1.0

Magnesium binding site 2 out of 3 in the Sequence Specific (Aatt) Orientation of Dapi 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 2 of Sequence Specific (Aatt) Orientation of Dapi Molecules at A Unique Minor Groove Binding Site (POSITION2) Within A Self-Assembled 3D Dna Lattice (4X5) within 5.0Å range:

Magnesium binding site 3 out of 3 in the Sequence Specific (Aatt) Orientation of Dapi 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 3 of Sequence Specific (Aatt) Orientation of Dapi 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:Mg102 b:119.0 occ:1.00 OP2 C:DG8 3.2 119.9 1.0 C8 C:DG8 4.0 109.0 1.0 C2' C:DT7 4.0 120.0 1.0 N7 C:DG8 4.2 113.8 1.0 C7 C:DT9 4.5 114.2 1.0 P C:DG8 4.6 135.5 1.0 C3' C:DT7 4.8 128.5 1.0 O5' C:DG8 4.8 117.9 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