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Arsenic in PDB 6xgk: Self-Assembly of A 3D Dna Crystal Lattice (4X5 Junction Version) Containing the J35 Immobile Holliday Junction

Protein crystallography data

The structure of Self-Assembly of A 3D Dna Crystal Lattice (4X5 Junction Version) Containing the J35 Immobile Holliday Junction, PDB code: 6xgk 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) 34.34 / 3.06
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 68.673, 68.673, 60.122, 90, 90, 120
R / Rfree (%) 19.7 / 21.1

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Self-Assembly of A 3D Dna Crystal Lattice (4X5 Junction Version) Containing the J35 Immobile Holliday Junction (pdb code 6xgk). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Self-Assembly of A 3D Dna Crystal Lattice (4X5 Junction Version) Containing the J35 Immobile Holliday Junction, PDB code: 6xgk:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 6xgk

Go back to Arsenic Binding Sites List in 6xgk
Arsenic binding site 1 out of 2 in the Self-Assembly of A 3D Dna Crystal Lattice (4X5 Junction Version) Containing the J35 Immobile Holliday Junction


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Self-Assembly of A 3D Dna Crystal Lattice (4X5 Junction Version) Containing the J35 Immobile Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As101

b:154.1
occ:1.00
N7 C:DG4 4.2 70.8 1.0
O6 C:DG4 4.3 79.9 1.0
OP2 C:DA3 4.5 64.7 1.0
N7 C:DA3 4.5 68.0 1.0
OP1 C:DA2 4.6 62.3 1.0
N6 C:DA3 4.9 82.4 1.0
C5 C:DA3 5.0 65.9 1.0
C5' C:DA2 5.0 69.2 1.0

Arsenic binding site 2 out of 2 in 6xgk

Go back to Arsenic Binding Sites List in 6xgk
Arsenic binding site 2 out of 2 in the Self-Assembly of A 3D Dna Crystal Lattice (4X5 Junction Version) Containing the J35 Immobile Holliday Junction


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Self-Assembly of A 3D Dna Crystal Lattice (4X5 Junction Version) Containing the J35 Immobile Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As101

b:140.2
occ:1.00
O6 B:DG15 3.7 88.4 1.0
O6 D:DG8 3.8 85.7 1.0
N7 D:DG8 4.3 76.7 1.0
C2' D:DT7 4.6 88.1 1.0
N4 D:DC9 4.7 74.5 1.0
C6 D:DG8 4.7 85.7 1.0
C6 B:DG15 4.7 79.9 1.0
O4 B:DT14 4.9 81.0 1.0
C5 D:DG8 4.9 75.9 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: Mon Jul 7 00:51:56 2025

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