Bromine in PDB 1v3n: Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex

The structure of Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex, PDB code: 1v3n was solved by J.Kondo, S.Umeda, T.Sunami, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.00 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	33.810, 43.470, 64.200, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 24.9

The structure of Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Bromine atom in the Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex (pdb code 1v3n). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex, PDB code: 1v3n:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex


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 D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br2 b:34.7 occ:1.00 BR A:CBR2 0.0 34.7 1.0 C5 A:CBR2 1.9 23.9 1.0 C6 A:CBR2 2.9 24.9 1.0 C4 A:CBR2 2.9 26.3 1.0 N4 A:CBR2 3.1 25.1 1.0 O6 A:DG3 3.5 26.4 1.0 C6 A:DG3 3.7 27.9 1.0 N1 A:DG3 3.8 29.2 1.0 O A:HOH37 3.8 38.4 1.0 C8 A:DG1 3.8 32.1 1.0 N7 A:DG1 4.0 31.8 1.0 N1 A:CBR2 4.1 30.2 1.0 O A:HOH17 4.2 18.5 1.0 N3 A:CBR2 4.2 26.5 1.0 O A:HOH48 4.3 40.5 1.0 N9 A:DG1 4.5 31.1 1.0 C5 A:DG3 4.5 24.9 1.0 C2 A:DG3 4.6 25.6 1.0 C2' A:DG1 4.7 35.7 1.0 C2 A:CBR2 4.7 24.3 1.0 C5 A:DG1 4.7 25.9 1.0 O A:HOH28 4.7 45.9 1.0 C4 A:DG1 5.0 27.6 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex


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 D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Br10 b:27.4 occ:1.00 BR B:CBR10 0.0 27.4 1.0 C5 B:CBR10 1.9 26.3 1.0 C6 B:CBR10 2.9 27.0 1.0 C4 B:CBR10 2.9 25.9 1.0 N4 B:CBR10 3.2 24.2 1.0 C6 B:DG11 3.5 22.4 1.0 O6 B:DG11 3.5 26.5 1.0 C8 B:DG9 3.5 28.4 1.0 N1 B:DG11 3.7 20.7 1.0 O B:HOH22 3.8 29.8 1.0 N7 B:DG9 3.9 27.8 1.0 C2' B:DG9 4.0 25.1 1.0 N9 B:DG9 4.0 28.6 1.0 C5 B:DG11 4.1 21.1 1.0 N1 B:CBR10 4.2 24.4 1.0 N3 B:CBR10 4.2 26.7 1.0 C2 B:DG11 4.3 20.2 1.0 C1' B:DG9 4.6 26.1 1.0 C5 B:DG9 4.6 27.4 1.0 C4 B:DG11 4.7 20.2 1.0 C4 B:DG9 4.7 26.1 1.0 C2 B:CBR10 4.7 25.3 1.0 N7 B:DG11 4.7 19.3 1.0 N3 B:DG11 4.9 20.5 1.0 N2 B:DG11 5.0 22.0 1.0

J.Kondo, W.Adachi, S.Umeda, T.Sunami, A.Takenaka. Crystal Structures of A Dna Octaplex with I-Motif of G-Quartets and Its Splitting Into Two Quadruplexes Suggest A Folding Mechanism of Eight Tandem Repeats Nucleic Acids Res. V. 32 2541 2004.
ISSN: ISSN 0305-1048
PubMed: 15133122
DOI: 10.1093/NAR/GKH575