Bromine in PDB 1k8p: Structure of the Human G-Quadruplex Reveals A Novel Topology

The structure of Structure of the Human G-Quadruplex Reveals A Novel Topology, PDB code: 1k8p was solved by G.N.Parkinson, M.P.H.Lee, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.607, 56.607, 40.546, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 28

The structure of Structure of the Human G-Quadruplex Reveals A Novel Topology also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Bromine atom in the Structure of the Human G-Quadruplex Reveals A Novel Topology (pdb code 1k8p). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Structure of the Human G-Quadruplex Reveals A Novel Topology, PDB code: 1k8p:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Structure of the Human G-Quadruplex Reveals A Novel Topology


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of the Human G-Quadruplex Reveals A Novel Topology within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1 b:31.4 occ:1.00 BR A:BRU1 0.0 31.4 1.0 C5 A:BRU1 1.9 46.1 1.0 C4 A:BRU1 2.8 48.3 1.0 C6 A:BRU1 2.9 59.4 1.0 O4 A:BRU1 3.0 50.5 1.0 N3 A:BRU1 4.1 51.3 1.0 N1 A:BRU1 4.1 64.2 1.0 O5' A:BRU1 4.7 91.9 1.0 C2 A:BRU1 4.7 53.9 1.0 O B:HOH2024 4.9 51.1 1.0

Bromine binding site 2 out of 4 in the Structure of the Human G-Quadruplex Reveals A Novel Topology


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of the Human G-Quadruplex Reveals A Novel Topology within 5.0Å range: probe atom residue distance (Å) B Occ A:Br6 b:36.5 occ:1.00 BR A:BRU6 0.0 36.5 1.0 C5 A:BRU6 1.9 46.5 1.0 C6 A:BRU6 2.8 47.4 1.0 C4 A:BRU6 2.8 52.3 1.0 O4 A:BRU6 3.0 55.9 1.0 O A:HOH2015 3.2 49.2 1.0 O A:HOH2001 3.3 45.1 1.0 O A:HOH2013 3.6 49.3 1.0 C2' A:DA8 3.8 37.4 1.0 O A:HOH2029 3.9 56.5 1.0 N9 A:DA8 3.9 54.6 1.0 C4 A:DA8 3.9 49.7 1.0 N3 A:BRU6 4.1 55.0 1.0 N1 A:BRU6 4.1 53.9 1.0 O A:HOH2003 4.2 44.3 1.0 N3 A:DA8 4.3 51.9 1.0 C8 A:DA8 4.3 54.0 1.0 C1' A:DA8 4.3 43.2 1.0 C5 A:DA8 4.3 47.8 1.0 O A:HOH2007 4.3 55.4 1.0 O A:HOH2042 4.4 60.9 1.0 C5' A:DG5 4.4 48.9 1.0 N7 A:DA8 4.5 54.1 1.0 O3' A:DG4 4.6 50.2 1.0 C1' A:DG4 4.6 50.2 1.0 C4' A:DG4 4.6 53.0 1.0 C2' A:DG4 4.7 48.9 1.0 C2 A:BRU6 4.7 57.0 1.0 O4' A:DG4 4.8 51.4 1.0 C2 A:DA8 4.8 59.2 1.0 O A:HOH2036 4.8 58.7 1.0 C6 A:DA8 4.9 51.0 1.0 C3' A:DG4 4.9 51.8 1.0 O4' A:DG5 5.0 47.7 1.0 C4' A:DG5 5.0 47.9 1.0

Bromine binding site 3 out of 4 in the Structure of the Human G-Quadruplex Reveals A Novel Topology


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of the Human G-Quadruplex Reveals A Novel Topology within 5.0Å range: probe atom residue distance (Å) B Occ B:Br13 b:19.1 occ:1.00 BR B:BRU13 0.0 19.1 1.0 C5 B:BRU13 1.9 39.5 1.0 C4 B:BRU13 2.8 42.3 1.0 C6 B:BRU13 2.9 36.8 1.0 O4 B:BRU13 3.0 43.1 1.0 N3 B:BRU13 4.1 39.5 1.0 N1 B:BRU13 4.2 41.3 1.0 O5' B:BRU13 4.5 41.4 1.0 O B:HOH2024 4.6 51.1 1.0 C2 B:BRU13 4.7 42.9 1.0

Bromine binding site 4 out of 4 in the Structure of the Human G-Quadruplex Reveals A Novel Topology


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of the Human G-Quadruplex Reveals A Novel Topology within 5.0Å range: probe atom residue distance (Å) B Occ B:Br18 b:39.5 occ:0.00 BR B:BRU18 0.0 39.5 0.0 C5 B:BRU18 1.9 39.5 0.0 C6 B:BRU18 2.9 39.5 0.0 C4 B:BRU18 2.9 39.5 0.0 O3' B:DG16 3.1 76.0 1.0 O4 B:BRU18 3.1 39.5 0.0 C4 B:DA20 3.7 39.5 0.0 OP1 B:DG17 3.7 86.8 1.0 N3 B:DA20 3.8 39.5 0.0 C4' B:DG16 3.9 67.6 1.0 C5 B:DA20 3.9 39.5 0.0 N9 B:DA20 3.9 39.5 0.0 P B:DG17 4.0 79.9 1.0 C3' B:DG16 4.1 68.2 1.0 C5' B:DG17 4.1 89.0 1.0 N3 B:BRU18 4.2 39.5 0.0 N1 B:BRU18 4.2 39.5 0.0 C2 B:DA20 4.2 39.5 0.0 C2' B:DA20 4.2 39.5 0.0 C6 B:DA20 4.3 39.5 0.0 C8 B:DA20 4.3 39.5 0.0 N7 B:DA20 4.4 39.5 0.0 N1 B:DA20 4.4 39.5 0.0 C1' B:DA20 4.5 39.5 0.0 O5' B:DG17 4.5 86.5 1.0 O4' B:DG16 4.6 66.8 1.0 C2 B:BRU18 4.8 39.5 0.0 O B:HOH2044 4.8 48.5 0.5 C5' B:DG16 4.8 61.5 1.0

G.N.Parkinson, M.P.Lee, S.Neidle. Crystal Structure of Parallel Quadruplexes From Human Telomeric Dna. Nature V. 417 876 2002.
ISSN: ISSN 0028-0836
PubMed: 12050675
DOI: 10.1038/NATURE755