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Magnesium in PDB 6wt1: Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J29 Immobile Holliday Junction

Protein crystallography data

The structure of Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J29 Immobile Holliday Junction, PDB code: 6wt1 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) 50.00 / 3.11
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 68.652, 68.652, 58.14, 90, 90, 120
R / Rfree (%) 21.8 / 25.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J29 Immobile Holliday Junction (pdb code 6wt1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J29 Immobile Holliday Junction, PDB code: 6wt1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6wt1

Go back to Magnesium Binding Sites List in 6wt1
Magnesium binding site 1 out of 2 in the Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J29 Immobile Holliday Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J29 Immobile Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:74.2
occ:1.00
OP2 B:DA1 3.0 86.5 1.0
N7 B:DG2 3.7 65.5 1.0
P B:DA1 3.9 115.0 1.0
O6 B:DG2 4.0 72.0 1.0
N7 B:DA1 4.3 73.1 1.0
C5 B:DG2 4.5 66.8 1.0
C6 B:DG2 4.7 72.0 1.0
C8 B:DG2 4.7 91.3 1.0
C8 B:DA1 4.8 77.0 1.0
OP1 B:DA1 4.9 114.8 1.0
C5 B:DA1 5.0 64.2 1.0

Magnesium binding site 2 out of 2 in 6wt1

Go back to Magnesium Binding Sites List in 6wt1
Magnesium binding site 2 out of 2 in the Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J29 Immobile Holliday Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Self-Assembly of A 3D Dna Crystal Lattice (4X5 Duplex Version) Containing the J29 Immobile Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:68.8
occ:1.00
O6 D:DG11 3.5 62.6 1.0
C7 D:DT10 4.0 101.2 1.0
N7 D:DG11 4.1 94.8 1.0
C6 D:DG11 4.4 66.6 1.0
C5 D:DG11 4.7 75.4 1.0
O4 D:DT10 4.7 81.7 1.0
C5 D:DT10 4.7 96.8 1.0
C4 D:DT10 5.0 92.2 1.0

Reference:

C.R.Simmons, T.Macculloch, N.Stephanopoulos, H.Yan. Structural and Computational Based Approach For the Creation of A Toolbox of Immobile Holliday Junctions For Dna-Directed Self-Assembly To Be Published.
Page generated: Sat Aug 21 15:12:01 2021

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