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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)

Protein crystallography data

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

Magnesium Binding Sites:

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 8tb4

Go back to Magnesium Binding Sites List in 8tb4
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 8tb4

Go back to Magnesium Binding Sites List in 8tb4
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 8tb4

Go back to Magnesium Binding Sites List in 8tb4
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

Reference:

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
Page generated: Fri Aug 15 16:18:49 2025

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