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

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

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

Arsenic	(As)	2 atoms
Potassium	(K)	14 atoms

The binding sites of Bromine atom in the G4(Br)UTTG4 Dimeric Quadruplex (pdb code 2avj). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the G4(Br)UTTG4 Dimeric Quadruplex, PDB code: 2avj:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br5 b:22.2 occ:0.50 BR A:BRU5 0.0 22.2 0.5 C5 A:BRU5 1.8 20.2 1.0 C6 A:BRU5 2.7 20.3 1.0 C4 A:BRU5 2.9 20.4 1.0 O4 A:BRU5 3.2 21.2 1.0 N1 A:BRU5 4.0 20.4 1.0 OP1 A:BRU5 4.0 22.4 1.0 N3 A:BRU5 4.1 19.3 1.0 C2 A:BRU5 4.6 19.9 1.0 O5' A:BRU5 4.6 23.4 1.0 P A:BRU5 5.0 21.9 1.0

Bromine binding site 2 out of 6 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Br16 b:19.7 occ:0.80 BR B:BRU16 0.0 19.7 0.8 C5 B:BRU16 1.8 18.9 1.0 C6 B:BRU16 2.7 18.8 1.0 C4 B:BRU16 2.9 18.7 1.0 O4 B:BRU16 3.1 19.8 1.0 C4' B:DG15 3.5 15.5 1.0 O B:HOH105 3.7 17.6 1.0 C5' B:DG15 3.8 15.7 1.0 O3' B:DG15 4.1 17.1 1.0 N1 B:BRU16 4.1 19.8 1.0 N3 B:BRU16 4.1 20.8 1.0 C3' B:DG15 4.3 15.8 1.0 O B:HOH186 4.5 25.1 1.0 O4' B:DG15 4.5 14.0 1.0 C2 B:BRU16 4.7 20.7 1.0

Bromine binding site 3 out of 6 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Br27 b:62.4 occ:0.10 BR C:BRU27 0.0 62.4 0.1 C5 C:BRU27 1.8 62.4 1.0 C6 C:BRU27 2.8 62.0 1.0 C4 C:BRU27 2.8 62.2 1.0 O4 C:BRU27 3.1 61.4 1.0 O C:HOH116 3.3 38.0 1.0 N3 C:DG26 3.4 30.1 1.0 C1' C:DG26 3.7 33.7 1.0 O C:HOH154 3.9 39.0 1.0 O3' C:DG26 4.0 43.6 1.0 N3 C:BRU27 4.1 62.0 1.0 N1 C:BRU27 4.1 60.8 1.0 C4 C:DG26 4.2 30.4 1.0 N2 C:DG26 4.2 29.5 1.0 C2 C:DG26 4.3 29.0 1.0 O4' C:DG26 4.3 35.9 1.0 N9 C:DG26 4.4 31.8 1.0 C2' C:DG26 4.5 36.3 1.0 C2 C:BRU27 4.7 61.4 1.0 C3' C:DG26 4.7 39.4 1.0 C4' C:DG26 4.7 37.7 1.0 OP1 C:BRU27 4.8 48.4 1.0

Bromine binding site 4 out of 6 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Br38 b:30.5 occ:0.50 BR D:BRU38 0.0 30.5 0.5 C5 D:BRU38 1.8 32.0 1.0 C6 D:BRU38 2.7 32.0 1.0 C4 D:BRU38 2.8 32.7 1.0 O4 D:BRU38 3.0 33.3 1.0 O D:HOH132 3.7 39.1 1.0 N1 D:BRU38 4.0 33.4 1.0 N3 D:BRU38 4.1 31.6 1.0 OP1 D:BRU38 4.4 36.5 1.0 O5' D:BRU38 4.6 36.0 1.0 C2 D:BRU38 4.6 33.0 1.0 O D:HOH228 4.9 42.3 1.0

Bromine binding site 5 out of 6 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ E:Br49 b:58.7 occ:0.10 BR E:BRU49 0.0 58.7 0.1 C5 E:BRU49 1.8 58.8 1.0 C6 E:BRU49 2.8 57.9 1.0 C4 E:BRU49 2.8 59.5 1.0 O4 E:BRU49 3.0 59.8 1.0 C7 E:DT50 3.4 53.0 1.0 O E:HOH203 3.5 44.2 1.0 C5 E:DT50 3.7 52.8 1.0 C6 E:DT50 3.8 52.9 1.0 N3 E:BRU49 4.1 59.5 1.0 N1 E:BRU49 4.1 58.0 1.0 O E:HOH208 4.6 31.5 1.0 C4 E:DT50 4.7 53.1 1.0 C2 E:BRU49 4.7 59.1 1.0 N1 E:DT50 4.8 52.1 1.0 C2' E:DT50 5.0 48.8 1.0

Bromine binding site 6 out of 6 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ F:Br60 b:35.2 occ:0.50 BR F:BRU60 0.0 35.2 0.5 C5 F:BRU60 1.8 33.9 1.0 C6 F:BRU60 2.7 32.7 1.0 C4 F:BRU60 2.8 33.7 1.0 O4 F:BRU60 3.1 32.9 1.0 K F:K78 3.6 21.4 1.0 N1 F:BRU60 4.0 32.4 1.0 N3 F:BRU60 4.1 33.7 1.0 C2 F:BRU60 4.6 33.4 1.0

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+