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Thallium in PDB 1s45: Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1

Protein crystallography data

The structure of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1, PDB code: 1s45 was solved by C.Caceres, G.Wright, C.Gouyette, G.Parkinson, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.50 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 28.259, 35.410, 32.057, 83.73, 61.78, 76.68
R / Rfree (%) 17.3 / 23.9

Other elements in 1s45:

The structure of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Sodium (Na) 1 atom

Thallium Binding Sites:

The binding sites of Thallium atom in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1 (pdb code 1s45). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 6 binding sites of Thallium where determined in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1, PDB code: 1s45:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6;

Thallium binding site 1 out of 6 in 1s45

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Thallium binding site 1 out of 6 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl1102

b:8.3
occ:0.60
O6 D:DG514 2.7 4.8 1.0
O6 B:DG294 2.8 7.5 1.0
O6 A:DG184 2.8 1.6 1.0
O6 C:DG404 2.8 6.8 1.0
O6 D:DG513 2.9 3.0 1.0
O6 B:DG293 2.9 7.3 1.0
O6 C:DG403 3.0 9.5 1.0
O6 A:DG183 3.2 11.2 1.0
TL A:TL1104 3.5 15.4 0.3
C6 D:DG514 3.6 6.6 1.0
C6 B:DG294 3.6 10.7 1.0
C6 D:DG513 3.7 4.8 1.0
C6 B:DG293 3.7 5.4 1.0
C6 A:DG184 3.7 1.8 1.0
C6 C:DG404 3.8 7.0 1.0
N1 B:DG294 3.8 9.3 1.0
C6 C:DG403 3.8 8.7 1.0
N1 D:DG514 3.9 4.5 1.0
C6 A:DG183 3.9 11.3 1.0
N1 A:DG184 3.9 1.6 1.0
N1 B:DG293 4.0 3.8 1.0
N1 D:DG513 4.0 4.2 1.0
N1 C:DG404 4.0 7.4 1.0
N1 C:DG403 4.1 7.1 1.0
N1 A:DG183 4.1 9.1 1.0
TL B:TL1106 4.2 11.4 0.1
C5 D:DG514 4.8 6.3 1.0
C5 D:DG513 4.8 2.5 1.0
C5 B:DG293 4.9 3.2 1.0
C5 B:DG294 5.0 11.1 1.0

Thallium binding site 2 out of 6 in 1s45

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Thallium binding site 2 out of 6 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 2 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl1104

b:15.4
occ:0.30
O6 A:DG182 2.7 5.8 1.0
O6 C:DG402 2.7 5.4 1.0
O6 D:DG513 2.7 3.0 1.0
O6 D:DG512 2.7 6.6 1.0
O6 B:DG292 2.8 4.3 1.0
O6 A:DG183 2.8 11.2 1.0
O6 B:DG293 2.8 7.3 1.0
O6 C:DG403 2.9 9.5 1.0
TL A:TL1105 3.3 7.7 0.3
TL A:TL1102 3.5 8.3 0.6
C6 A:DG182 3.5 9.6 1.0
C6 D:DG512 3.6 9.6 1.0
C6 B:DG292 3.6 6.7 1.0
C6 C:DG402 3.6 3.9 1.0
C6 D:DG513 3.7 4.8 1.0
C6 C:DG403 3.8 8.7 1.0
C6 B:DG293 3.8 5.4 1.0
C6 A:DG183 3.8 11.3 1.0
N1 B:DG292 3.8 3.6 1.0
N1 A:DG182 3.8 8.8 1.0
N1 D:DG512 3.8 7.9 1.0
N1 C:DG402 3.9 2.3 1.0
N1 A:DG183 4.0 9.1 1.0
N1 C:DG403 4.0 7.1 1.0
N1 B:DG293 4.0 3.8 1.0
N1 D:DG513 4.0 4.2 1.0
C5 A:DG182 4.8 9.9 1.0
C5 D:DG512 4.8 9.7 1.0
C5 C:DG402 4.9 3.0 1.0
C5 B:DG292 4.9 6.3 1.0
C5 D:DG513 4.9 2.5 1.0

Thallium binding site 3 out of 6 in 1s45

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Thallium binding site 3 out of 6 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 3 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl1105

b:7.7
occ:0.30
O6 G:DG842 2.7 4.4 1.0
O6 H:DG952 2.7 2.1 1.0
O6 F:DG732 2.8 5.8 1.0
O6 E:DG622 2.8 8.5 1.0
O6 C:DG402 2.8 5.4 1.0
O6 D:DG512 2.8 6.6 1.0
O6 A:DG182 2.9 5.8 1.0
O6 B:DG292 2.9 4.3 1.0
TL A:TL1104 3.3 15.4 0.3
TL E:TL1103 3.5 8.6 0.7
C6 C:DG402 3.6 3.9 1.0
C6 H:DG952 3.6 5.0 1.0
C6 D:DG512 3.7 9.6 1.0
C6 A:DG182 3.7 9.6 1.0
C6 B:DG292 3.7 6.7 1.0
C6 G:DG842 3.7 5.9 1.0
C6 F:DG732 3.8 7.3 1.0
C6 E:DG622 3.8 6.5 1.0
N1 D:DG512 3.9 7.9 1.0
N1 B:DG292 3.9 3.6 1.0
N1 C:DG402 3.9 2.3 1.0
N1 A:DG182 3.9 8.8 1.0
N1 H:DG952 3.9 3.3 1.0
N1 G:DG842 4.0 5.3 1.0
N1 F:DG732 4.1 9.5 1.0
N1 E:DG622 4.2 6.9 1.0
C5 C:DG402 4.9 3.0 1.0
C5 D:DG512 4.9 9.7 1.0
C5 A:DG182 4.9 9.9 1.0
C5 B:DG292 4.9 6.3 1.0
C5 H:DG952 4.9 5.2 1.0

Thallium binding site 4 out of 6 in 1s45

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Thallium binding site 4 out of 6 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 4 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl1106

b:11.4
occ:0.15
O6 B:DG295 2.3 7.8 1.0
O6 A:DG185 2.3 14.9 1.0
O6 C:DG405 2.4 7.5 1.0
O6 D:DG515 2.5 11.6 1.0
O A:HOH1108 2.9 10.1 1.0
C6 B:DG295 3.2 8.5 1.0
O6 D:DG514 3.4 4.8 1.0
C6 C:DG405 3.4 8.5 1.0
C6 A:DG185 3.4 13.2 1.0
N1 B:DG295 3.4 7.7 1.0
O6 B:DG294 3.5 7.5 1.0
C6 D:DG515 3.6 10.3 1.0
N1 C:DG405 3.6 7.3 1.0
O6 C:DG404 3.6 6.8 1.0
O6 A:DG184 3.7 1.6 1.0
N1 A:DG185 3.8 13.3 1.0
N1 D:DG515 3.9 8.7 1.0
C6 D:DG514 4.1 6.6 1.0
C6 B:DG294 4.1 10.7 1.0
TL A:TL1102 4.2 8.3 0.6
C6 C:DG404 4.3 7.0 1.0
C6 A:DG184 4.3 1.8 1.0
N1 D:DG514 4.4 4.5 1.0
N1 A:DG184 4.4 1.6 1.0
N1 B:DG294 4.4 9.3 1.0
N1 C:DG404 4.4 7.4 1.0
C5 B:DG295 4.6 9.3 1.0
C5 A:DG185 4.7 12.1 1.0
C2 B:DG295 4.7 7.8 1.0
C5 C:DG405 4.8 9.6 1.0
C5 D:DG515 4.9 9.9 1.0
C2 C:DG405 4.9 9.6 1.0

Thallium binding site 5 out of 6 in 1s45

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Thallium binding site 5 out of 6 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 5 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Tl1101

b:12.1
occ:0.60
O6 E:DG624 2.7 4.7 1.0
O6 F:DG734 2.7 10.2 1.0
O6 H:DG954 2.8 9.8 1.0
O6 G:DG844 2.8 3.7 1.0
O6 F:DG733 2.9 6.9 1.0
O6 G:DG843 2.9 9.9 1.0
O6 E:DG623 3.0 11.1 1.0
O6 H:DG953 3.1 8.9 1.0
C6 E:DG624 3.6 5.3 1.0
C6 F:DG734 3.6 9.4 1.0
TL E:TL1103 3.6 8.6 0.7
C6 F:DG733 3.7 11.3 1.0
C6 G:DG843 3.7 9.2 1.0
C6 G:DG844 3.7 6.2 1.0
C6 H:DG954 3.7 11.8 1.0
C6 H:DG953 3.8 9.8 1.0
C6 E:DG623 3.8 10.9 1.0
N1 H:DG953 3.9 10.5 1.0
N1 F:DG734 3.9 9.2 1.0
N1 E:DG624 3.9 3.1 1.0
N1 F:DG733 3.9 12.0 1.0
N1 G:DG844 4.0 6.8 1.0
N1 G:DG843 4.0 7.7 1.0
NA E:NA1107 4.0 6.3 1.0
N1 H:DG954 4.1 10.2 1.0
N1 E:DG623 4.1 10.5 1.0
C5 E:DG624 4.9 4.8 1.0
C5 F:DG734 4.9 8.4 1.0
C5 F:DG733 4.9 10.5 1.0
C5 G:DG843 4.9 10.1 1.0
C5 E:DG623 4.9 10.3 1.0
C5 H:DG953 5.0 7.7 1.0

Thallium binding site 6 out of 6 in 1s45

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Thallium binding site 6 out of 6 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 6 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt) S1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Tl1103

b:8.6
occ:0.70
O6 G:DG843 2.9 9.9 1.0
O6 H:DG953 2.9 8.9 1.0
O6 E:DG623 2.9 11.1 1.0
O6 F:DG733 2.9 6.9 1.0
O6 H:DG952 3.0 2.1 1.0
O6 F:DG732 3.0 5.8 1.0
O6 E:DG622 3.1 8.5 1.0
O6 G:DG842 3.2 4.4 1.0
TL A:TL1105 3.5 7.7 0.3
TL E:TL1101 3.6 12.1 0.6
C6 H:DG953 3.7 9.8 1.0
C6 G:DG843 3.7 9.2 1.0
C6 F:DG732 3.7 7.3 1.0
C6 H:DG952 3.7 5.0 1.0
C6 F:DG733 3.8 11.3 1.0
C6 E:DG623 3.8 10.9 1.0
C6 G:DG842 3.8 5.9 1.0
N1 H:DG953 3.9 10.5 1.0
C6 E:DG622 3.9 6.5 1.0
N1 G:DG843 3.9 7.7 1.0
N1 H:DG952 3.9 3.3 1.0
N1 F:DG733 4.0 12.0 1.0
N1 E:DG623 4.0 10.5 1.0
N1 G:DG842 4.0 5.3 1.0
N1 F:DG732 4.0 9.5 1.0
N1 E:DG622 4.2 6.9 1.0
C5 F:DG732 4.8 8.0 1.0
C5 G:DG842 4.9 6.8 1.0
C5 H:DG952 4.9 5.2 1.0
C5 E:DG622 5.0 6.7 1.0
C5 G:DG843 5.0 10.1 1.0

Reference:

C.Caceres, G.Wright, C.Gouyette, G.Parkinson, J.A.Subirana. A Thymine Tetrad in D(Tggggt) Quadruplexes Stabilized with Tl+1/Na+1 Ions Nucleic Acids Res. V. 32 1097 2004.
ISSN: ISSN 0305-1048
PubMed: 14960719
DOI: 10.1093/NAR/GKH269
Page generated: Wed Dec 16 02:28:36 2020

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