Atomistry » Thallium » PDB 1f1h-4wfh » 4en5
Atomistry »
  Thallium »
    PDB 1f1h-4wfh »
      4en5 »

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

Go back to Thallium Binding Sites List in 4en5
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

Go back to Thallium Binding Sites List in 4en5
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

Go back to Thallium Binding Sites List in 4en5
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

Go back to Thallium Binding Sites List in 4en5
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

Go back to Thallium Binding Sites List in 4en5
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

Go back to Thallium Binding Sites List in 4en5
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: Wed Dec 16 02:28:43 2020

Last articles

Zn in 7OQY
Zn in 7PEL
Zn in 7OYG
Zn in 7P3S
Zn in 7PE7
Zn in 7RZC
Zn in 7PE9
Zn in 7PE8
Zn in 7RAG
Zn in 7RN5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy