Bromine in PDB 1gqu: Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing

The structure of Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing, PDB code: 1gqu was solved by N.G.A.Abrescia, A.Thompson, T.Huynh-Dinh, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.5
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	23.960, 48.950, 32.240, 90.00, 93.27, 90.00
R / Rfree (%)	22 / n/a

The binding sites of Bromine atom in the Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing (pdb code 1gqu). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing, PDB code: 1gqu:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing within 5.0Å range: probe atom residue distance (Å) B Occ A:Br4 b:36.3 occ:1.00 BR A:BRU4 0.0 36.3 1.0 C5 A:BRU4 1.6 22.5 1.0 C6 A:BRU4 2.5 22.5 1.0 C4 A:BRU4 2.6 22.5 1.0 O4 A:BRU4 3.0 22.5 1.0 N3 A:DA3 3.5 18.7 1.0 C4 A:DA3 3.6 18.7 1.0 O A:HOH2007 3.6 28.2 1.0 C2' A:DA3 3.7 30.3 1.0 N6 A:DA5 3.7 19.8 1.0 N3 A:BRU4 3.8 22.5 1.0 N1 A:BRU4 3.8 22.5 1.0 C2 A:DA3 3.9 18.7 1.0 N9 A:DA3 3.9 18.7 1.0 C6 A:DA5 4.0 19.8 1.0 O A:HOH2011 4.0 20.3 1.0 C5 A:DA3 4.0 18.7 1.0 N1 A:DA5 4.1 19.8 1.0 O A:HOH2010 4.2 22.5 1.0 N1 A:DA3 4.3 18.7 1.0 C1' A:DA3 4.3 30.3 1.0 C2 A:BRU4 4.4 22.5 1.0 C6 A:DA3 4.4 18.7 1.0 C8 A:DA3 4.6 18.7 1.0 N7 A:DA3 4.7 18.7 1.0 C5 A:DA5 5.0 19.8 1.0 C2 A:DA5 5.0 19.8 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing within 5.0Å range: probe atom residue distance (Å) B Occ B:Br10 b:31.2 occ:1.00 BR B:BRU10 0.0 31.2 1.0 C5 B:BRU10 1.6 24.1 1.0 C6 B:BRU10 2.5 24.1 1.0 C4 B:BRU10 2.6 24.1 1.0 O4 B:BRU10 3.0 24.1 1.0 N6 B:DA11 3.5 22.5 1.0 C4 B:DA9 3.7 19.9 1.0 O B:HOH2002 3.7 39.2 1.0 O B:HOH2008 3.7 17.5 1.0 O B:HOH2010 3.8 17.9 1.0 N3 B:DA9 3.8 19.9 1.0 O B:HOH2001 3.8 36.2 1.0 N3 B:BRU10 3.8 24.1 1.0 N1 B:BRU10 3.9 24.1 1.0 C5 B:DA9 4.0 19.9 1.0 C6 B:DA11 4.0 22.5 1.0 C2 B:DA9 4.0 19.9 1.0 N1 B:DA11 4.1 22.5 1.0 N9 B:DA9 4.1 19.9 1.0 C2' B:DA9 4.2 14.2 1.0 C6 B:DA9 4.2 19.9 1.0 N1 B:DA9 4.3 19.9 1.0 C2 B:BRU10 4.4 24.1 1.0 N7 B:DA9 4.5 19.9 1.0 C8 B:DA9 4.6 19.9 1.0 O B:HOH2006 4.6 14.0 1.0 C1' B:DA9 4.7 14.2 1.0 C5 B:DA11 4.9 22.5 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing within 5.0Å range: probe atom residue distance (Å) B Occ C:Br16 b:37.4 occ:1.00 BR C:BRU16 0.0 37.4 1.0 C5 C:BRU16 1.6 13.7 1.0 C6 C:BRU16 2.5 13.7 1.0 C4 C:BRU16 2.6 13.7 1.0 O4 C:BRU16 3.0 13.7 1.0 N3 C:DA15 3.6 18.5 1.0 O C:HOH2004 3.7 40.7 1.0 C4 C:DA15 3.7 18.5 1.0 N1 C:BRU16 3.8 13.7 1.0 N3 C:BRU16 3.8 13.7 1.0 C2 C:DA15 3.9 18.5 1.0 C2' C:DA15 3.9 21.3 1.0 N9 C:DA15 4.2 18.5 1.0 C5 C:DA15 4.2 18.5 1.0 N1 A:DA1 4.3 12.7 1.0 N1 C:DA15 4.3 18.5 1.0 C2 C:BRU16 4.4 13.7 1.0 C6 C:DA15 4.5 18.5 1.0 C1' C:DA15 4.6 21.3 1.0 C2 A:DA1 4.8 12.7 1.0 C8 C:DA15 4.8 18.5 1.0 N7 C:DA15 4.9 18.5 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of An Alternating A-T Oligonucleotide Fragment with Hoogsteen Base Pairing within 5.0Å range: probe atom residue distance (Å) B Occ D:Br22 b:38.4 occ:1.00 BR D:BRU22 0.0 38.4 1.0 C5 D:BRU22 1.6 11.5 1.0 C6 D:BRU22 2.5 11.5 1.0 C4 D:BRU22 2.6 11.5 1.0 O4 D:BRU22 3.0 11.5 1.0 N3 D:DA21 3.6 22.1 1.0 C4 D:DA21 3.7 22.1 1.0 N1 D:DA23 3.7 43.1 1.0 N6 D:DA23 3.7 43.1 1.0 N1 D:BRU22 3.8 11.5 1.0 N3 D:BRU22 3.8 11.5 1.0 C2 D:DA21 3.8 22.1 1.0 O D:HOH2007 3.9 24.4 1.0 C2' D:DA21 4.1 25.4 1.0 C6 D:DA23 4.1 43.1 1.0 C5 D:DA21 4.1 22.1 1.0 O D:HOH2010 4.2 39.9 1.0 N9 D:DA21 4.2 22.1 1.0 N1 D:DA21 4.2 22.1 1.0 C2 D:BRU22 4.4 11.5 1.0 C6 D:DA21 4.4 22.1 1.0 C1' D:DA21 4.7 25.4 1.0 C2 D:DA23 4.7 43.1 1.0 C8 D:DA21 4.8 22.1 1.0 N7 D:DA21 4.8 22.1 1.0

N.G.A.Abrescia, A.Thompson, T.Huynh-Dinh, J.A.Subirana. Crystal Structure of An Antiparallel Dna Fragment with Hoogsteen Base Pairing Proc.Natl.Acad.Sci.Usa V. 99 2806 2002.
ISSN: ISSN 0027-8424
PubMed: 11880632
DOI: 10.1073/PNAS.052675499