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Bromine 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:

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

Bromine Binding Sites:

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 2avj

Go back to Bromine Binding Sites List in 2avj
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 2avj

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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 2avj

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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 2avj

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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 2avj

Go back to Bromine Binding Sites List in 2avj
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 2avj

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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

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: Mon Jul 7 04:04:04 2025

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