Bromine in PDB 3qxr: Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna

The structure of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna, PDB code: 3qxr was solved by D.Wei, G.N.Parkinson, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.90 / 1.62
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	37.570, 51.350, 58.340, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 21.3

The structure of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Potassium	(K)	9 atoms

The binding sites of Bromine atom in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna (pdb code 3qxr). 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 the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna, PDB code: 3qxr:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


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 the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Br12 b:17.6 occ:1.00 BR A:BRU12 0.0 17.6 1.0 C5 A:BRU12 1.9 13.6 1.0 C6 A:BRU12 2.8 14.2 1.0 C4 A:BRU12 2.9 13.8 1.0 O4 A:BRU12 3.1 12.6 1.0 C5' A:DC11 3.4 15.7 0.5 O A:HOH49 3.4 21.1 1.0 N3 A:DG10 3.7 11.1 1.0 O4' A:DG10 3.7 12.6 1.0 O B:HOH33 3.7 14.4 1.0 O B:HOH210 3.7 18.0 1.0 N3 B:DG6 3.7 14.1 1.0 C1' A:DG10 3.9 10.2 1.0 N2 B:DG6 3.9 10.5 1.0 C3' A:DC11 3.9 16.3 0.5 C2 B:DG6 3.9 13.1 1.0 C5' A:DC11 4.0 18.2 0.5 C4 A:DG10 4.1 11.1 1.0 C3' A:DC11 4.1 17.8 0.5 N1 A:BRU12 4.1 13.5 1.0 N3 A:BRU12 4.1 11.6 1.0 N9 A:DG10 4.2 9.1 1.0 O A:HOH53 4.2 16.4 1.0 C2' A:DC11 4.2 17.6 0.5 C4' A:DC11 4.2 17.3 0.5 O B:HOH36 4.2 15.0 1.0 C2' A:DC11 4.3 14.6 0.5 C2 A:DG10 4.4 11.7 1.0 C4 B:DG6 4.4 13.4 1.0 O5' A:DC11 4.6 16.0 0.5 C2 A:BRU12 4.6 16.4 1.0 N1 B:DG6 4.7 10.7 1.0 C4' A:DC11 4.7 18.7 0.5 N2 A:DG10 4.7 13.0 1.0 C4' A:DG10 4.8 12.9 1.0 O5' A:BRU12 5.0 19.9 1.0 N9 B:DG6 5.0 15.2 1.0 C1' B:DG6 5.0 18.0 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


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 the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Br12 b:11.4 occ:1.00 BR B:BRU12 0.0 11.4 1.0 C5 B:BRU12 1.9 10.6 1.0 C6 B:BRU12 2.9 12.8 1.0 C4 B:BRU12 2.9 10.1 1.0 O2 B:DC11 3.0 10.6 1.0 O4 B:BRU12 3.1 12.3 1.0 O B:HOH48 3.4 10.3 1.0 N2 B:DG10 3.5 8.6 1.0 C6 A:DG6 3.5 7.9 1.0 C2 B:DG10 3.5 7.4 1.0 C5 A:DG6 3.6 10.1 1.0 K A:K25 3.6 11.4 1.0 O6 A:DG6 3.6 7.9 1.0 N1 B:DG10 3.8 8.5 1.0 N1 A:DG6 3.9 8.4 1.0 C1' B:DC11 4.0 11.1 1.0 C2' B:DC11 4.0 9.3 1.0 N3 B:DG10 4.0 9.7 1.0 N7 A:DG6 4.0 9.7 1.0 C2 B:DC11 4.1 11.4 1.0 C4 A:DG6 4.2 10.0 1.0 N1 B:BRU12 4.2 14.7 1.0 N3 B:BRU12 4.2 11.2 1.0 O3' B:DC11 4.4 14.6 1.0 C2 A:DG6 4.4 8.8 1.0 OP2 B:BRU12 4.6 15.7 1.0 N1 B:DC11 4.6 10.1 1.0 C4 B:DG10 4.6 8.8 1.0 C6 B:DG10 4.6 11.6 1.0 N3 A:DG6 4.6 8.8 1.0 N7 B:DG13 4.6 8.9 1.0 C8 A:DG6 4.6 9.0 1.0 C2 B:BRU12 4.7 14.7 1.0 O5' B:BRU12 4.7 18.1 1.0 N9 A:DG6 4.7 10.5 1.0 C3' B:DC11 4.8 11.5 1.0 O6 B:DG13 4.9 8.6 1.0 N1 A:DG2 4.9 10.9 1.0 P B:BRU12 4.9 21.1 1.0 C5 B:DG10 4.9 8.9 1.0 O6 A:DG10 5.0 8.3 1.0

D.Wei, G.N.Parkinson, A.P.Reszka, S.Neidle. Crystal Structure of A C-Kit Promoter Quadruplex Reveals the Structural Role of Metal Ions and Water Molecules in Maintaining Loop Conformation. Nucleic Acids Res. V. 40 4691 2012.
ISSN: ISSN 0305-1048
PubMed: 22287624
DOI: 10.1093/NAR/GKS023