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

Protein crystallography data

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

Other elements in 1k8p:

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

Bromine Binding Sites:

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 1k8p

Go back to Bromine Binding Sites List in 1k8p
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 1k8p

Go back to Bromine Binding Sites List in 1k8p
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 1k8p

Go back to Bromine Binding Sites List in 1k8p
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 1k8p

Go back to Bromine Binding Sites List in 1k8p
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

Reference:

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
Page generated: Wed Jul 10 16:47:57 2024

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