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Thallium in PDB 2hbn: Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex

Protein crystallography data

The structure of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex, PDB code: 2hbn was solved by M.L.Gill, S.A.Strobel, J.P.Loria, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.11 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 27.375, 48.210, 96.198, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 24.8

Thallium Binding Sites:

The binding sites of Thallium atom in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex (pdb code 2hbn). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 10 binding sites of Thallium where determined in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex, PDB code: 2hbn:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Thallium binding site 1 out of 10 in 2hbn

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Thallium binding site 1 out of 10 in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl114

b:27.3
occ:1.00
 O6 B:DG2 2.5 23.9 1.0
O6 A:DG2 2.6 28.2 1.0
O6 A:DG10 2.8 23.4 1.0
O6 A:DG3 2.9 19.9 1.0
O6 B:DG11 2.9 20.9 1.0
O6 A:DG11 3.0 23.0 1.0
O6 B:DG3 3.0 23.1 1.0
O6 B:DG10 3.0 25.8 1.0
C6 B:DG2 3.4 21.2 1.0
C6 A:DG2 3.5 27.5 1.0
TL A:TL116 3.5 28.9 1.0
TL A:TL115 3.5 26.7 1.0
C6 A:DG10 3.6 22.9 1.0
C6 B:DG10 3.7 23.9 1.0
N1 B:DG2 3.8 21.5 1.0
N1 B:DG10 3.8 24.2 1.0
C6 A:DG3 3.8 21.7 1.0
N1 A:DG2 3.9 26.8 1.0
N1 A:DG10 3.9 22.1 1.0
C6 A:DG11 3.9 19.0 1.0
C6 B:DG11 3.9 23.4 1.0
C6 B:DG3 3.9 22.2 1.0
N1 B:DG11 4.1 23.7 1.0
N1 A:DG11 4.1 22.7 1.0
N1 A:DG3 4.1 20.9 1.0
N1 B:DG3 4.2 24.0 1.0
C5 B:DG2 4.6 23.0 1.0
C5 A:DG2 4.7 27.3 1.0
C5 A:DG10 4.8 23.4 1.0
C5 B:DG10 4.9 24.6 1.0

Thallium binding site 2 out of 10 in 2hbn

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Thallium binding site 2 out of 10 in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 2 of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl115

b:26.7
occ:1.00
 O6 B:DG1 2.7 21.9 1.0
O6 B:DG12 2.8 21.9 1.0
O6 A:DG3 2.9 19.9 1.0
O6 A:DG9 2.9 25.1 1.0
O6 B:DG11 2.9 20.9 1.0
O6 A:DG4 2.9 25.2 1.0
O6 B:DG2 3.0 23.9 1.0
O6 A:DG10 3.0 23.4 1.0
C6 A:DG3 3.5 21.7 1.0
C6 B:DG1 3.5 16.6 1.0
TL A:TL114 3.5 27.3 1.0
TL A:TL117 3.6 34.7 1.0
C6 B:DG11 3.7 23.4 1.0
C6 B:DG12 3.7 23.2 1.0
C6 A:DG9 3.7 24.2 1.0
N1 B:DG1 3.7 18.0 1.0
C6 A:DG4 3.8 23.4 1.0
N1 A:DG3 3.8 20.9 1.0
C6 A:DG10 3.9 22.9 1.0
C6 B:DG2 3.9 21.2 1.0
N1 A:DG4 3.9 23.5 1.0
N1 B:DG11 3.9 23.7 1.0
N1 B:DG12 4.0 22.7 1.0
N1 A:DG9 4.0 24.9 1.0
N1 B:DG2 4.2 21.5 1.0
N1 A:DG10 4.2 22.1 1.0
C5 A:DG3 4.7 21.2 1.0
C5 B:DG1 4.8 19.2 1.0
C5 B:DG11 4.8 23.5 1.0
C5 A:DG9 4.9 24.5 1.0
C5 B:DG12 4.9 23.4 1.0
C2 A:DG3 5.0 21.3 1.0

Thallium binding site 3 out of 10 in 2hbn

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Thallium binding site 3 out of 10 in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 3 of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl116

b:28.9
occ:1.00
 O6 A:DG1 2.7 26.1 1.0
O6 B:DG4 2.8 27.7 1.0
O6 A:DG11 2.8 23.0 1.0
O6 A:DG12 2.9 26.4 1.0
O6 B:DG10 3.0 25.8 1.0
O6 B:DG3 3.0 23.1 1.0
O6 B:DG9 3.1 26.8 1.0
O6 A:DG2 3.1 28.2 1.0
C6 A:DG11 3.5 19.0 1.0
TL A:TL114 3.5 27.3 1.0
C6 A:DG1 3.6 24.2 1.0
C6 B:DG4 3.7 27.2 1.0
TL B:TL113 3.7 41.6 1.0
C6 B:DG3 3.7 22.2 1.0
C6 A:DG12 3.8 25.7 1.0
C6 B:DG9 3.8 26.6 1.0
N1 A:DG11 3.8 22.7 1.0
N1 A:DG1 3.8 25.9 1.0
C6 B:DG10 3.8 23.9 1.0
N1 B:DG3 3.9 24.0 1.0
N1 B:DG4 3.9 27.1 1.0
C6 A:DG2 4.0 27.5 1.0
N1 B:DG9 4.1 27.3 1.0
N1 A:DG12 4.1 25.7 1.0
N1 B:DG10 4.1 24.2 1.0
N1 A:DG2 4.3 26.8 1.0
C5 A:DG11 4.7 22.6 1.0
C5 A:DG1 4.8 26.0 1.0
C5 B:DG3 4.9 23.3 1.0
C5 B:DG4 5.0 26.7 1.0
C5 B:DG9 5.0 26.7 1.0

Thallium binding site 4 out of 10 in 2hbn

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Thallium binding site 4 out of 10 in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 4 of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl117

b:34.7
occ:1.00
 O2 A:DT7 2.6 25.9 1.0
O2 A:DT5 2.7 28.0 1.0
O6 A:DG9 3.0 25.1 1.0
O6 B:DG12 3.0 21.9 1.0
O6 A:DG4 3.1 25.2 1.0
O A:HOH118 3.1 22.5 1.0
O6 B:DG1 3.2 21.9 1.0
C2 A:DT5 3.5 27.1 1.0
C2 A:DT7 3.5 24.6 1.0
N3 A:DT5 3.6 27.6 1.0
TL A:TL115 3.6 26.7 1.0
C6 B:DG12 3.7 23.2 1.0
N3 A:DT7 3.8 21.9 1.0
C6 A:DG4 3.8 23.4 1.0
C6 A:DG9 3.9 24.2 1.0
C6 B:DG1 3.9 16.6 1.0
N1 B:DG12 4.0 22.7 1.0
N1 B:DG1 4.1 18.0 1.0
N1 A:DG9 4.1 24.9 1.0
O2 A:DT6 4.1 27.6 1.0
N1 A:DG4 4.2 23.5 1.0
C2 A:DT6 4.5 25.5 1.0
N3 A:DT6 4.6 25.2 1.0
N1 A:DT7 4.8 24.3 1.0
O4' A:DT8 4.8 31.3 1.0
C5 B:DG12 4.8 23.4 1.0
C5 A:DG4 4.9 24.7 1.0
N1 A:DT5 4.9 28.6 1.0
C4 A:DT5 4.9 27.4 1.0

Thallium binding site 5 out of 10 in 2hbn

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Thallium binding site 5 out of 10 in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 5 of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl113

b:41.6
occ:1.00
 O2 B:DT7 2.5 27.8 1.0
O2 B:DT5 2.7 30.7 1.0
O6 A:DG12 2.8 26.4 1.0
O6 B:DG9 3.0 26.8 1.0
O6 B:DG4 3.1 27.7 1.0
O6 A:DG1 3.4 26.1 1.0
C2 B:DT7 3.4 28.2 1.0
C2 B:DT5 3.6 30.1 1.0
C6 A:DG12 3.6 25.7 1.0
TL A:TL116 3.7 28.9 1.0
N3 B:DT7 3.7 27.8 1.0
N3 B:DT5 3.8 29.4 1.0
C6 B:DG9 3.8 26.6 1.0
C6 B:DG4 3.9 27.2 1.0
O B:HOH115 3.9 25.9 1.0
O2 B:DT6 3.9 28.9 1.0
N1 A:DG12 4.0 25.7 1.0
N1 B:DG9 4.0 27.3 1.0
C6 A:DG1 4.1 24.2 1.0
N1 A:DG1 4.2 25.9 1.0
N1 B:DG4 4.3 27.1 1.0
C2 B:DT6 4.4 29.1 1.0
N3 B:DT6 4.6 28.6 1.0
N1 B:DT7 4.7 29.3 1.0
C5 A:DG12 4.8 24.0 1.0
O4' B:DT8 4.9 34.2 1.0
N1 B:DT5 4.9 30.1 1.0
C5 B:DG4 4.9 26.7 1.0

Thallium binding site 6 out of 10 in 2hbn

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Thallium binding site 6 out of 10 in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 6 of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl118

b:28.8
occ:1.00
 O6 D:DG3 2.6 23.3 1.0
O6 C:DG2 2.7 23.1 1.0
O6 D:DG2 2.8 22.3 1.0
O6 C:DG11 2.9 26.7 1.0
O6 D:DG10 2.9 23.9 1.0
O6 C:DG10 2.9 23.2 1.0
O6 C:DG3 3.0 26.0 1.0
O6 D:DG11 3.1 23.2 1.0
C6 C:DG2 3.5 23.5 1.0
TL C:TL120 3.5 29.9 1.0
TL C:TL119 3.5 28.3 1.0
C6 D:DG2 3.6 21.8 1.0
C6 C:DG10 3.6 25.4 1.0
C6 D:DG10 3.6 22.9 1.0
C6 D:DG3 3.7 21.7 1.0
N1 C:DG10 3.7 25.9 1.0
C6 C:DG11 3.8 27.0 1.0
N1 D:DG10 3.8 23.9 1.0
N1 D:DG2 3.8 21.7 1.0
N1 C:DG2 3.8 23.7 1.0
C6 C:DG3 3.9 24.7 1.0
C6 D:DG11 4.0 24.4 1.0
N1 C:DG11 4.0 27.3 1.0
N1 D:DG11 4.1 23.6 1.0
N1 D:DG3 4.1 22.4 1.0
N1 C:DG3 4.2 26.5 1.0
C5 C:DG2 4.7 22.7 1.0
C5 D:DG2 4.8 23.7 1.0
C5 C:DG10 4.8 24.7 1.0
C5 D:DG10 4.9 24.2 1.0
C2 C:DG10 5.0 25.7 1.0
C5 D:DG3 5.0 23.6 1.0

Thallium binding site 7 out of 10 in 2hbn

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Thallium binding site 7 out of 10 in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 7 of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl119

b:28.3
occ:1.00
 O6 C:DG1 2.5 25.8 1.0
O6 D:DG4 2.6 24.4 1.0
O6 C:DG11 2.8 26.7 1.0
O6 D:DG9 2.9 23.4 1.0
O6 C:DG12 2.9 24.7 1.0
O6 D:DG3 2.9 23.3 1.0
O6 C:DG2 3.0 23.1 1.0
O6 D:DG10 3.1 23.9 1.0
C6 C:DG11 3.5 27.0 1.0
C6 C:DG1 3.5 22.5 1.0
TL C:TL118 3.5 28.8 1.0
C6 D:DG3 3.6 21.7 1.0
C6 D:DG4 3.6 25.5 1.0
C6 D:DG9 3.7 21.6 1.0
TL D:TL121 3.7 40.3 1.0
C6 C:DG12 3.8 25.4 1.0
N1 C:DG1 3.8 22.3 1.0
N1 D:DG3 3.8 22.4 1.0
N1 D:DG4 3.9 23.6 1.0
N1 C:DG11 3.9 27.3 1.0
N1 D:DG9 3.9 24.0 1.0
C6 D:DG10 3.9 22.9 1.0
C6 C:DG2 4.0 23.5 1.0
N1 C:DG12 4.0 23.7 1.0
N1 D:DG10 4.2 23.9 1.0
N1 C:DG2 4.2 23.7 1.0
C5 C:DG11 4.7 28.0 1.0
C5 D:DG3 4.7 23.6 1.0
C5 C:DG1 4.8 22.8 1.0
C5 D:DG9 4.9 22.2 1.0
C5 D:DG4 4.9 25.9 1.0

Thallium binding site 8 out of 10 in 2hbn

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Thallium binding site 8 out of 10 in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 8 of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl120

b:29.9
occ:1.00
 O6 C:DG9 2.7 24.2 1.0
O6 C:DG4 2.8 28.3 1.0
O6 D:DG1 2.8 25.6 1.0
O6 D:DG12 2.9 18.4 1.0
O6 C:DG3 2.9 26.0 1.0
O6 C:DG10 3.0 23.2 1.0
O6 D:DG2 3.0 22.3 1.0
O6 D:DG11 3.1 23.2 1.0
TL C:TL118 3.5 28.8 1.0
C6 C:DG9 3.6 24.4 1.0
C6 C:DG3 3.6 24.7 1.0
TL C:TL122 3.7 37.9 1.0
C6 D:DG1 3.7 23.8 1.0
C6 D:DG11 3.7 24.4 1.0
C6 C:DG4 3.7 27.8 1.0
C6 C:DG10 3.8 25.4 1.0
C6 D:DG12 3.8 20.1 1.0
N1 C:DG3 3.9 26.5 1.0
N1 C:DG4 3.9 27.7 1.0
N1 D:DG11 3.9 23.6 1.0
C6 D:DG2 3.9 21.8 1.0
N1 C:DG9 3.9 23.5 1.0
N1 D:DG1 4.0 25.1 1.0
N1 C:DG10 4.1 25.9 1.0
N1 D:DG12 4.1 21.7 1.0
N1 D:DG2 4.1 21.7 1.0
C5 C:DG9 4.8 24.4 1.0
C5 C:DG3 4.8 26.6 1.0
C5 D:DG11 4.9 23.7 1.0
C5 D:DG1 4.9 24.7 1.0

Thallium binding site 9 out of 10 in 2hbn

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Thallium binding site 9 out of 10 in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 9 of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl122

b:37.9
occ:1.00
 O2 C:DT7 2.5 25.7 1.0
O2 C:DT5 2.8 28.3 1.0
O6 C:DG9 2.9 24.2 1.0
O6 C:DG4 3.1 28.3 1.0
O6 D:DG12 3.2 18.4 1.0
O6 D:DG1 3.3 25.6 1.0
C2 C:DT7 3.5 27.2 1.0
C2 C:DT5 3.6 28.9 1.0
TL C:TL120 3.7 29.9 1.0
N3 C:DT5 3.7 29.0 1.0
C6 C:DG9 3.7 24.4 1.0
N3 C:DT7 3.8 26.8 1.0
C6 C:DG4 3.9 27.8 1.0
C6 D:DG12 3.9 20.1 1.0
N1 C:DG9 4.0 23.5 1.0
O2 C:DT6 4.0 30.9 1.0
C6 D:DG1 4.1 23.8 1.0
N1 D:DG12 4.2 21.7 1.0
N1 D:DG1 4.2 25.1 1.0
N1 C:DG4 4.2 27.7 1.0
O C:HOH124 4.3 20.1 1.0
C2 C:DT6 4.4 31.4 1.0
N3 C:DT6 4.5 31.2 1.0
N1 C:DT7 4.8 28.4 1.0
O4' C:DT8 4.8 33.2 1.0
C5 C:DG4 4.9 28.6 1.0
C5 C:DG9 4.9 24.4 1.0
C4 C:DT5 5.0 29.8 1.0
N1 C:DT5 5.0 30.8 1.0

Thallium binding site 10 out of 10 in 2hbn

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Thallium binding site 10 out of 10 in the Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 10 of Crystallization of the Tl+-Form of the Oxytricha Nova G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Tl121

b:40.3
occ:1.00
 O2 D:DT7 2.5 26.6 1.0
O6 C:DG12 2.8 24.7 1.0
O2 D:DT5 2.9 31.2 1.0
O6 D:DG9 3.0 23.4 1.0
O6 D:DG4 3.3 24.4 1.0
O6 C:DG1 3.4 25.8 1.0
O D:HOH122 3.5 25.3 1.0
C2 D:DT7 3.5 26.3 1.0
N3 D:DT5 3.5 31.3 1.0
C2 D:DT5 3.6 30.3 1.0
C6 C:DG12 3.6 25.4 1.0
O2 D:DT6 3.7 26.6 1.0
TL C:TL119 3.7 28.3 1.0
C6 D:DG9 3.8 21.6 1.0
N3 D:DT7 3.8 26.6 1.0
N1 D:DG9 3.9 24.0 1.0
N1 C:DG12 4.0 23.7 1.0
C6 D:DG4 4.0 25.5 1.0
C6 C:DG1 4.2 22.5 1.0
C2 D:DT6 4.2 27.9 1.0
N1 C:DG1 4.3 22.3 1.0
N3 D:DT6 4.3 28.6 1.0
N1 D:DG4 4.4 23.6 1.0
O4' D:DT8 4.5 29.7 1.0
N1 D:DT7 4.8 26.9 1.0
C4 D:DT5 4.8 31.1 1.0
C5 C:DG12 4.8 25.4 1.0
N1 D:DT5 4.9 31.6 1.0
C5 D:DG4 4.9 25.9 1.0
C5 D:DG9 5.0 22.2 1.0

Reference:

M.L.Gill, S.A.Strobel, J.P.Loria. Crystallization and Characterization of the Thallium Form of the Oxytricha Nova G-Quadruplex. Nucleic Acids Res. V. 34 4506 2006.
ISSN: ISSN 0305-1048
PubMed: 16945956
DOI: 10.1093/NAR/GKL616
Page generated: Fri Oct 11 09:37:50 2024

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