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Thallium in PDB 3ggi: Locating Monovalent Cations in One Turn of G/C Rich B-Dna

Protein crystallography data

The structure of Locating Monovalent Cations in One Turn of G/C Rich B-Dna, PDB code: 3ggi was solved by T.Maehigashi, T.Moulaei, D.Watkins, S.Komeda, L.D.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.31 / 0.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 32.277, 25.204, 34.095, 90.00, 116.10, 90.00
R / Rfree (%) 11.8 / 14.4

Other elements in 3ggi:

The structure of Locating Monovalent Cations in One Turn of G/C Rich B-Dna also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Thallium Binding Sites:

The binding sites of Thallium atom in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna (pdb code 3ggi). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 6 binding sites of Thallium where determined in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna, PDB code: 3ggi:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6;

Thallium binding site 1 out of 6 in 3ggi

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Thallium binding site 1 out of 6 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl101

b:7.3
occ:0.24
 O A:HOH287 0.8 6.9 0.4
TL A:TL105 2.5 12.8 0.1
MG A:MG22 2.6 8.2 0.4
N7 A:DG9 2.8 6.0 1.0
O A:HOH261 2.9 10.8 0.5
O A:HOH284 2.9 8.9 0.4
O A:HOH259 3.0 7.2 0.5
O6 A:DG10 3.0 5.5 1.0
O A:HOH286 3.2 8.9 0.4
O A:HOH285 3.6 9.7 0.4
O A:HOH283 3.6 11.4 0.5
C8 A:DG9 3.7 6.2 1.0
C5 A:DG9 3.7 4.9 1.0
O A:HOH283 3.8 9.4 0.4
O6 A:DG9 3.8 5.6 1.0
C6 A:DG10 4.0 4.8 1.0
O A:HOH267 4.0 9.6 0.4
C6 A:DG9 4.1 4.9 1.0
O A:HOH287 4.2 8.2 0.5
TL A:TL104 4.3 11.7 0.1
N7 A:DG10 4.4 5.4 1.0
C5 A:DG10 4.5 4.7 1.0
O A:HOH286 4.7 10.1 0.5
C2' A:DT8 4.7 6.0 1.0
O A:HOH288 4.7 8.9 0.4
N9 A:DG9 4.8 5.6 1.0
C4 A:DG9 4.8 4.8 1.0
MG A:MG22 4.9 9.8 0.5
O A:HOH227 5.0 12.5 0.5

Thallium binding site 2 out of 6 in 3ggi

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Thallium binding site 2 out of 6 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 2 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl102

b:14.1
occ:0.11
 O A:HOH282 1.6 10.1 0.8
MG A:MG21 1.8 8.5 0.8
O A:HOH279 1.9 11.0 0.8
O A:HOH278 2.1 8.7 0.8
O6 A:DG4 2.7 5.8 1.0
N7 A:DA3 3.0 5.2 1.0
N7 A:DG4 3.0 6.3 1.0
O A:HOH277 3.4 12.4 0.8
C6 A:DG4 3.4 5.2 1.0
O A:HOH280 3.4 8.6 0.8
C5 A:DG4 3.5 5.7 1.0
O A:HOH204 3.5 9.1 1.0
C8 A:DA3 3.6 5.1 1.0
O A:HOH281 3.6 10.4 0.8
C5 A:DA3 4.0 4.7 1.0
C8 A:DG4 4.2 6.1 1.0
O A:HOH222 4.3 15.8 1.0
OP2 A:DA3 4.4 5.1 0.7
TL A:TL103 4.4 11.4 0.2
N6 A:DA3 4.5 5.0 1.0
C6 A:DA3 4.6 4.5 1.0
N9 A:DA3 4.7 4.6 1.0
N1 A:DG4 4.7 5.6 1.0
C4 A:DG4 4.8 5.2 1.0
C4 A:DA3 4.9 4.3 1.0

Thallium binding site 3 out of 6 in 3ggi

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Thallium binding site 3 out of 6 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 3 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl103

b:11.4
occ:0.16
 O A:HOH238 1.8 7.9 0.3
O6 A:DG5 2.1 8.1 0.3
O6 A:DG5 2.7 5.2 0.7
O A:HOH238 3.0 9.3 0.3
C6 A:DG5 3.3 7.5 0.3
N7 A:DG4 3.4 6.3 1.0
O A:HOH279 3.4 11.0 0.8
C6 A:DG5 3.9 4.3 0.7
C8 A:DG4 3.9 6.1 1.0
C5 A:DG4 4.0 5.7 1.0
C5 A:DG5 4.2 7.4 0.3
N1 A:DG5 4.2 7.4 0.3
C6 A:DG4 4.4 5.2 1.0
O6 A:DG4 4.4 5.8 1.0
TL A:TL102 4.4 14.1 0.1
N7 A:DG5 4.4 7.8 0.3
N7 A:DG5 4.5 5.7 0.7
C5 A:DG5 4.6 4.7 0.7
O A:HOH277 4.6 12.4 0.8
N9 A:DG4 4.7 6.0 1.0
C4 A:DG4 4.7 5.2 1.0
N4 A:DC6 4.8 10.6 0.3
O A:HOH282 4.8 10.1 0.8
N1 A:DG5 5.0 4.5 0.7

Thallium binding site 4 out of 6 in 3ggi

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Thallium binding site 4 out of 6 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 4 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl104

b:11.7
occ:0.06
 O A:HOH287 0.8 8.2 0.5
TL A:TL105 2.1 12.8 0.1
MG A:MG22 2.9 9.8 0.5
O A:HOH284 3.3 8.9 0.4
O A:HOH285 3.4 11.4 0.5
O A:HOH284 3.5 8.6 0.5
O A:HOH283 3.6 11.4 0.5
O A:HOH286 3.9 10.1 0.5
TL A:TL101 4.3 7.3 0.2
O6 A:DG10 4.3 5.5 1.0
O A:HOH287 4.8 6.9 0.4

Thallium binding site 5 out of 6 in 3ggi

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Thallium binding site 5 out of 6 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 5 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl105

b:12.8
occ:0.06
 TL A:TL104 2.1 11.7 0.1
O A:HOH287 2.3 8.2 0.5
TL A:TL101 2.5 7.3 0.2
O6 A:DG10 2.7 5.5 1.0
O A:HOH284 3.0 8.9 0.4
O A:HOH287 3.1 6.9 0.4
O A:HOH283 3.5 11.4 0.5
C6 A:DG10 3.8 4.8 1.0
MG A:MG22 3.9 9.8 0.5
MG A:MG22 4.1 8.2 0.4
N7 A:DG10 4.3 5.4 1.0
O A:HOH286 4.4 10.1 0.5
C5 A:DG10 4.4 4.7 1.0
O A:HOH285 4.5 9.7 0.4
O A:HOH285 4.6 11.4 0.5
N7 A:DG9 4.7 6.0 1.0
O A:HOH259 4.8 7.2 0.5
O A:HOH286 4.8 8.9 0.4
N1 A:DG10 4.9 4.8 1.0
O A:HOH261 4.9 10.8 0.5

Thallium binding site 6 out of 6 in 3ggi

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Thallium binding site 6 out of 6 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 6 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl106

b:14.7
occ:0.12
 O A:HOH296 0.4 11.1 0.3
O A:HOH300 0.9 5.4 0.1
MG A:MG24 1.9 5.0 0.1
MG A:MG24 1.9 10.0 0.3
O A:HOH298 2.2 5.5 0.1
O A:HOH300 2.4 11.2 0.3
O A:HOH274 2.7 7.3 0.2
O A:HOH300 2.8 9.9 0.3
O A:HOH297 2.8 10.7 0.3
O A:HOH296 2.9 5.2 0.1
O A:HOH295 2.9 5.7 0.1
O A:HOH298 3.0 11.0 0.3
O A:HOH299 3.1 10.0 0.3
O A:HOH276 3.2 7.0 0.2
O A:HOH241 3.3 7.3 0.3
O A:HOH297 3.5 5.1 0.1
O A:HOH265 3.7 11.1 0.4
O A:HOH298 3.8 9.4 0.3
O A:HOH299 4.0 5.5 0.1
MG A:MG24 4.1 10.0 0.3
O A:HOH295 4.1 11.1 0.3
O A:HOH296 4.2 10.6 0.3
O A:HOH241 4.4 7.5 0.1
N2 A:DG4 4.6 6.5 1.0
O A:HOH234 4.7 9.2 0.3
O A:HOH240 4.8 11.6 0.3
O A:HOH239 4.9 15.0 0.4

Reference:

T.Maehigashi, T.Moulaei, D.Watkins, S.Komeda, L.D.Williams. Locating Monovalent Cations in One Turn of G/C Rich B-Dna To Be Published.
Page generated: Fri Oct 11 09:47:26 2024

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