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Arsenic in PDB 2avj: G4(Br)UTTG4 Dimeric Quadruplex

Protein crystallography data

The structure of G4(Br)UTTG4 Dimeric Quadruplex, PDB code: 2avj was solved by P.Hazel, G.N.Parkinson, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.40 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 31.681, 33.309, 79.234, 90.00, 91.49, 90.00
R / Rfree (%) 16.8 / 24.2

Other elements in 2avj:

The structure of G4(Br)UTTG4 Dimeric Quadruplex also contains other interesting chemical elements:

Bromine (Br) 6 atoms
Potassium (K) 14 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the G4(Br)UTTG4 Dimeric Quadruplex (pdb code 2avj). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the G4(Br)UTTG4 Dimeric Quadruplex, PDB code: 2avj:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 2avj

Go back to Arsenic Binding Sites List in 2avj
Arsenic binding site 1 out of 2 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As81

b:28.8
occ:1.00
C8 D:DG43 3.9 26.5 1.0
C8 D:DG36 3.9 29.0 1.0
C1' D:DG36 4.2 29.7 1.0
O E:HOH169 4.3 22.6 1.0
O4' D:DG44 4.3 26.6 1.0
C5' D:DG37 4.4 32.4 1.0
N9 D:DG36 4.4 29.3 1.0
O4' D:DG37 4.4 32.0 1.0
C4' D:DG37 4.5 32.6 1.0
C4' D:DG44 4.5 26.6 1.0
C1' D:DG43 4.6 28.0 1.0
C5' D:DG44 4.6 27.7 1.0
N9 D:DG43 4.6 27.8 1.0
O4' D:DG36 4.6 31.8 1.0
N7 D:DG43 4.8 26.1 1.0
N7 D:DG36 4.9 28.2 1.0

Arsenic binding site 2 out of 2 in 2avj

Go back to Arsenic Binding Sites List in 2avj
Arsenic binding site 2 out of 2 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As82

b:20.1
occ:1.00
C8 D:DG34 3.8 21.5 1.0
C4' D:DG35 4.0 29.3 1.0
C8 E:DG45 4.0 22.7 1.0
O4' D:DG35 4.1 28.6 1.0
C5' D:DG35 4.1 28.2 1.0
C1' D:DG34 4.1 22.1 1.0
C5' E:DG46 4.2 26.1 1.0
O4' E:DG46 4.2 26.4 1.0
C4' E:DG46 4.3 26.9 1.0
N9 D:DG34 4.3 22.1 1.0
O E:HOH123 4.4 20.9 1.0
C1' E:DG45 4.4 23.9 1.0
O4' D:DG34 4.6 22.0 1.0
N9 E:DG45 4.6 23.3 1.0
O4' E:DG45 4.8 24.6 1.0
N7 D:DG34 4.8 20.2 1.0
O E:HOH127 4.9 18.5 1.0

Reference:

P.Hazel, G.N.Parkinson, S.Neidle. Topology Variation and Loop Structural Homology in Crystal and Simulated Structures of A Bimolecular Dna Quadruplex. J.Am.Chem.Soc. V. 128 5480 2006.
ISSN: ISSN 0002-7863
PubMed: 16620121
DOI: 10.1021/JA058577+
Page generated: Tue Oct 27 16:48:39 2020

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