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Thallium in PDB 4en5: Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked

Protein crystallography data

The structure of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked, PDB code: 4en5 was solved by A.M.Ren, K.R.Rajashankar, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.36 / 2.96
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.205, 77.287, 42.597, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.1

Other elements in 4en5:

The structure of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked also contains other interesting chemical elements:

Fluorine (F) 1 atom
Magnesium (Mg) 9 atoms

Thallium Binding Sites:

The binding sites of Thallium atom in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked (pdb code 4en5). 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 of Fluoride Riboswitch, Tl-Acetate Soaked, PDB code: 4en5:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6;

Thallium binding site 1 out of 6 in 4en5

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Thallium binding site 1 out of 6 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl111

b:0.8
occ:1.00
 O A:HOH220 2.5 81.8 1.0
O6 A:G39 2.5 66.1 1.0
O A:HOH222 2.5 69.3 1.0
O A:HOH219 2.5 75.2 1.0
O A:HOH221 2.5 67.2 1.0
N7 A:G39 3.2 61.6 1.0
C6 A:G39 3.2 62.4 1.0
C5 A:G39 3.5 61.4 1.0
O4 A:U38 4.0 61.7 1.0
N3 A:U7 4.3 56.3 1.0
C4 A:U38 4.3 61.4 1.0
C8 A:G39 4.4 61.7 1.0
N1 A:G39 4.5 56.6 1.0
C5 A:U38 4.5 62.4 1.0
O4 A:U7 4.8 57.5 1.0
C4 A:G39 4.8 60.0 1.0
C2 A:U7 4.8 59.4 1.0
C4 A:U7 4.8 55.4 1.0
O2 A:U7 4.8 61.8 1.0
O A:HOH213 4.9 56.1 1.0

Thallium binding site 2 out of 6 in 4en5

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Thallium binding site 2 out of 6 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 2 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl112

b:0.6
occ:1.00
 O A:HOH232 2.5 97.7 1.0
O A:HOH231 2.5 88.7 1.0
O A:HOH233 2.5 98.5 1.0
O A:HOH235 2.5 83.7 1.0
O A:HOH234 2.5 79.0 1.0
O6 A:G3 3.2 80.0 1.0
N7 A:G3 3.2 72.9 1.0
N7 A:G2 3.7 78.0 1.0
O6 A:G2 3.8 82.3 1.0
C6 A:G3 3.8 76.3 1.0
C5 A:G2 3.9 78.4 1.0
C5 A:G3 3.9 73.5 1.0
C6 A:G2 3.9 79.6 1.0
C8 A:G3 4.3 72.8 1.0
C8 A:G2 4.4 79.2 1.0
O A:HOH216 4.4 77.2 1.0
OP1 A:G2 4.6 86.3 1.0
C4 A:G2 4.7 76.8 1.0
N4 A:C4 4.8 77.2 1.0
N1 A:G2 4.8 74.2 1.0
N9 A:G2 5.0 76.5 1.0

Thallium binding site 3 out of 6 in 4en5

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Thallium binding site 3 out of 6 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 3 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl113

b:0.6
occ:1.00
 O A:HOH228 2.5 71.4 1.0
O A:HOH227 2.5 83.8 1.0
O6 A:G42 2.6 86.5 1.0
O A:HOH226 2.7 81.5 1.0
N7 A:G42 3.0 78.7 1.0
C6 A:G42 3.4 84.6 1.0
C5 A:G42 3.6 80.3 1.0
O6 A:G5 3.7 78.3 1.0
C6 A:G5 3.9 79.8 1.0
N7 A:G5 3.9 75.1 1.0
C5 A:G5 3.9 77.3 1.0
C8 A:G42 4.1 78.6 1.0
O A:HOH201 4.3 84.5 1.0
C8 A:G5 4.7 71.0 1.0
N1 A:G5 4.7 78.7 1.0
O6 A:G43 4.7 87.8 1.0
O2' A:U41 4.8 73.7 1.0
N1 A:G42 4.8 82.8 1.0
C4 A:G5 4.8 76.8 1.0
MG A:MG104 4.9 72.4 1.0
C4 A:G42 4.9 78.9 1.0
O3' A:U41 5.0 66.3 1.0
OP1 A:G42 5.0 64.8 1.0

Thallium binding site 4 out of 6 in 4en5

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Thallium binding site 4 out of 6 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 4 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl114

b:0.7
occ:1.00
 O A:HOH225 2.5 71.5 1.0
O A:HOH223 2.5 76.5 1.0
O A:HOH201 2.5 84.5 1.0
O6 A:G10 2.5 85.0 1.0
O A:HOH224 2.5 82.1 1.0
O6 A:G11 2.5 89.1 1.0
C6 A:G10 3.1 81.5 1.0
N7 A:G10 3.3 78.7 1.0
C5 A:G10 3.4 79.1 1.0
C6 A:G11 3.6 87.4 1.0
N7 A:G11 3.9 84.0 1.0
C5 A:G11 4.1 85.7 1.0
N6 A:A9 4.3 73.5 1.0
N1 A:G10 4.3 82.8 1.0
C8 A:G10 4.4 79.1 1.0
O A:HOH227 4.5 83.8 1.0
C6 A:A9 4.5 72.0 1.0
C4 A:G10 4.7 79.0 1.0
N4 A:C12 4.7 85.8 1.0
C5 A:A9 4.7 69.7 1.0
O6 A:G43 4.8 87.8 1.0
N1 A:G11 4.8 86.4 1.0
N7 A:A9 4.8 66.6 1.0

Thallium binding site 5 out of 6 in 4en5

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Thallium binding site 5 out of 6 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 5 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl115

b:0.1
occ:1.00
 O A:HOH208 2.5 67.1 1.0
O A:HOH230 2.5 61.7 1.0
O A:HOH209 2.5 52.7 1.0
O A:HOH229 2.5 64.7 1.0
O A:HOH207 2.5 69.3 1.0
O6 A:G35 2.5 57.3 1.0
N7 A:G35 3.0 57.8 1.0
MG A:MG106 3.1 53.5 1.0
MG A:MG107 3.2 54.6 1.0
C6 A:G35 3.3 56.5 1.0
N7 A:G34 3.4 56.9 1.0
C5 A:G35 3.5 56.4 1.0
O6 A:G34 3.6 58.0 1.0
C5 A:G34 3.8 53.7 1.0
C6 A:G34 3.9 54.5 1.0
C8 A:G35 4.3 58.9 1.0
C8 A:G34 4.3 56.4 1.0
N1 A:G35 4.6 55.8 1.0
O6 A:G36 4.7 54.7 1.0
C4 A:G34 4.8 54.9 1.0
N4 A:C26 4.8 58.4 1.0
C4 A:G35 4.8 56.5 1.0
N7 A:G36 4.9 57.3 1.0
N1 A:G34 4.9 54.7 1.0

Thallium binding site 6 out of 6 in 4en5

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Thallium binding site 6 out of 6 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 6 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl116

b:0.6
occ:1.00
 OP1 A:U7 2.4 67.2 1.0
O A:HOH218 2.5 66.5 1.0
O A:HOH202 2.5 68.2 1.0
OP1 A:G5 2.5 71.6 1.0
O A:HOH203 2.5 66.1 1.0
O3' A:A6 2.6 63.1 1.0
OP1 A:A6 3.0 65.5 1.0
O5' A:A6 3.0 60.9 1.0
P A:U7 3.1 56.2 1.0
P A:A6 3.5 58.3 1.0
P A:G5 3.6 64.2 1.0
F A:F110 3.7 67.4 1.0
C3' A:A6 3.8 62.2 1.0
O5' A:G5 4.0 63.3 1.0
MG A:MG103 4.0 61.7 1.0
C4' A:A6 4.0 63.0 1.0
OP2 A:U7 4.1 59.2 1.0
C5' A:A6 4.1 65.7 1.0
OP2 A:G5 4.2 67.7 1.0
OP2 A:A6 4.2 66.5 1.0
O5' A:U7 4.2 56.5 1.0
C5' A:G5 4.3 65.2 1.0
MG A:MG104 4.3 72.4 1.0
C5' A:U7 4.3 61.2 1.0
OP1 A:G8 4.4 61.5 1.0
OP2 A:G8 4.8 60.2 1.0
MG A:MG102 4.8 60.4 1.0
O3' A:G5 4.9 67.1 1.0
O2' A:A6 4.9 64.2 1.0
O3' A:C4 4.9 69.3 1.0
C2' A:A6 5.0 61.6 1.0

Reference:

A.Ren, K.R.Rajashankar, D.J.Patel. Fluoride Ion Encapsulation By MG2+ Ions and Phosphates in A Fluoride Riboswitch. Nature V. 486 85 2012.
ISSN: ISSN 0028-0836
PubMed: 22678284
DOI: 10.1038/NATURE11152
Page generated: Fri Oct 11 09:57:57 2024

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