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Thallium in PDB 3oxm: Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked

Protein crystallography data

The structure of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked, PDB code: 3oxm was solved by L.Huang, A.Serganov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.95
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.783, 83.783, 200.066, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 22.5

Other elements in 3oxm:

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

Magnesium (Mg) 27 atoms

Thallium Binding Sites:

The binding sites of Thallium atom in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked (pdb code 3oxm). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 10 binding sites of Thallium where determined in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked, PDB code: 3oxm:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Thallium binding site 1 out of 10 in 3oxm

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Thallium binding site 1 out of 10 in the Crystal Structure of Glycine 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 Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl201

b:0.3
occ:0.50
 O2' B:U20 3.1 80.1 1.0
O4 B:U18 3.1 51.8 1.0
O2 B:U20 3.3 77.4 1.0
O4 B:U23 3.5 78.8 1.0
OP2 B:A22 3.6 92.4 1.0
O6 B:G17 3.7 47.5 1.0
C2 B:U20 3.9 77.8 1.0
N4 B:C24 4.1 46.6 1.0
C4 B:U18 4.1 52.4 1.0
C1' B:U20 4.1 79.3 1.0
C2' B:U20 4.1 80.3 1.0
C5 B:U23 4.2 77.3 1.0
C4 B:U23 4.2 77.8 1.0
N1 B:U20 4.3 78.5 1.0
C6 B:G17 4.4 47.9 1.0
O3' B:U20 4.5 84.1 1.0
C5 B:U18 4.6 52.4 1.0
C4 B:C24 4.7 47.4 1.0
N1 B:G17 4.8 47.8 1.0
N3 B:U20 4.8 77.8 1.0
N3 B:C24 4.8 48.1 1.0
C3' B:U20 5.0 81.0 1.0
P B:A22 5.0 92.0 1.0

Thallium binding site 2 out of 10 in 3oxm

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Thallium binding site 2 out of 10 in the Crystal Structure of Glycine 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 Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl202

b:0.0
occ:1.00
 N7 B:G25 3.1 44.0 1.0
O6 B:G25 3.2 44.0 1.0
C5 B:G25 3.7 44.1 1.0
N7 B:G26 3.7 42.3 1.0
C6 B:G25 3.8 44.0 1.0
N4 B:C24 4.0 46.6 1.0
O6 B:G26 4.1 41.3 1.0
C4 B:C24 4.1 47.4 1.0
C8 B:G25 4.2 44.3 1.0
C5 B:C24 4.2 47.7 1.0
OP2 B:U23 4.2 82.0 1.0
OP1 B:U23 4.4 81.5 1.0
C5 B:G26 4.5 42.2 1.0
C6 B:G26 4.6 41.7 1.0
C8 B:G26 4.7 43.0 1.0
P B:U23 4.7 82.1 1.0
N3 B:C24 4.8 48.1 1.0
C6 B:C24 4.9 48.8 1.0
C4 B:G25 5.0 44.6 1.0

Thallium binding site 3 out of 10 in 3oxm

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Thallium binding site 3 out of 10 in the Crystal Structure of Glycine 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 Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl203

b:0.4
occ:0.80
 O6 B:G80 2.8 52.5 1.0
O6 B:G8 3.1 50.2 1.0
N7 B:G8 3.2 48.1 1.0
C6 B:G8 3.7 48.8 1.0
C5 B:G8 3.8 48.0 1.0
C6 B:G80 3.8 51.2 1.0
TL B:TL208 4.2 0.9 0.2
C8 B:G8 4.3 47.2 1.0
C5 B:G80 4.7 51.0 1.0
OP2 B:G7 4.7 51.1 1.0
N1 B:G80 4.7 50.3 1.0
N7 B:G80 4.8 51.6 1.0
N7 B:G7 4.9 50.2 1.0

Thallium binding site 4 out of 10 in 3oxm

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Thallium binding site 4 out of 10 in the Crystal Structure of Glycine 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 Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl204

b:0.0
occ:1.00
 O6 A:G80 2.8 62.3 1.0
N7 A:G8 3.0 57.1 1.0
O6 A:G8 3.0 59.7 1.0
C5 A:G8 3.6 57.3 1.0
C6 A:G8 3.6 58.2 1.0
C6 A:G80 3.9 61.5 1.0
C8 A:G8 4.1 56.4 1.0
OP2 A:G7 4.6 60.9 1.0
N1 A:G80 4.6 60.8 1.0
N7 A:G7 4.7 59.5 1.0
C5 A:G80 4.9 61.5 1.0
C4 A:G8 4.9 56.6 1.0
N1 A:G8 4.9 57.9 1.0

Thallium binding site 5 out of 10 in 3oxm

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Thallium binding site 5 out of 10 in the Crystal Structure of Glycine 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 Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl205

b:0.2
occ:1.00
 OP2 A:A71 2.5 72.1 1.0
OP2 A:C70 2.6 71.7 1.0
O3' A:U69 3.5 69.7 1.0
P A:C70 3.5 71.9 1.0
O6 A:G72 3.6 57.7 1.0
N7 A:G72 3.8 59.3 1.0
O2' A:U69 3.8 66.5 1.0
O5' A:C70 3.9 72.6 1.0
P A:A71 3.9 72.5 1.0
N7 A:A71 4.0 66.2 1.0
TL A:TL207 4.3 43.0 0.1
C6 A:G72 4.4 57.2 1.0
C8 A:A71 4.4 67.3 1.0
O5' A:A71 4.4 71.3 1.0
C5 A:G72 4.5 58.1 1.0
C3' A:U69 4.6 68.2 1.0
OP1 A:A71 4.8 73.9 1.0
C2' A:U69 4.8 66.8 1.0
C3' A:C70 4.9 73.4 1.0
O3' A:C70 4.9 73.7 1.0
C8 A:G72 4.9 59.6 1.0
OP1 A:C70 4.9 72.3 1.0

Thallium binding site 6 out of 10 in 3oxm

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Thallium binding site 6 out of 10 in the Crystal Structure of Glycine 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 Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl206

b:0.0
occ:0.80
 O6 A:G42 2.5 58.1 1.0
N7 A:G42 3.3 57.7 1.0
N4 A:C43 3.3 66.9 1.0
O6 A:G60 3.4 82.6 1.0
N2 A:G62 3.4 61.0 1.0
C6 A:G42 3.4 58.8 1.0
OP2 A:A41 3.7 59.5 1.0
C5 A:G42 3.7 58.3 1.0
O4 A:U61 3.7 74.0 1.0
C2 A:G62 3.8 62.0 1.0
N7 A:A41 3.8 55.7 1.0
MG A:MG128 4.1 70.6 1.0
C4 A:C43 4.1 67.5 1.0
N3 A:U61 4.2 75.0 1.0
C8 A:A41 4.2 54.8 1.0
N1 A:G62 4.3 62.8 1.0
N3 A:G62 4.3 62.8 1.0
C6 A:G60 4.4 83.8 1.0
C4 A:U61 4.4 75.4 1.0
C8 A:G42 4.5 57.5 1.0
N3 A:C43 4.5 68.8 1.0
N1 A:G42 4.7 59.9 1.0
O5' A:A41 4.8 57.8 1.0
P A:A41 4.9 58.7 1.0
C5 A:A41 4.9 55.6 1.0
C5 A:C43 5.0 67.2 1.0
N1 A:G60 5.0 84.0 1.0

Thallium binding site 7 out of 10 in 3oxm

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Thallium binding site 7 out of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 7 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl207

b:43.0
occ:0.05
 O6 A:G73 2.8 59.3 1.0
N7 A:G73 3.2 58.4 1.0
C6 A:G73 3.6 58.1 1.0
C5 A:G73 3.7 57.8 1.0
N7 A:G72 3.9 59.3 1.0
O6 A:G72 4.1 57.7 1.0
TL A:TL205 4.3 0.2 1.0
C5 A:G72 4.3 58.1 1.0
C6 A:G72 4.4 57.2 1.0
C8 A:G73 4.4 57.7 1.0
C8 A:G72 4.7 59.6 1.0
N1 A:G73 4.9 57.2 1.0

Thallium binding site 8 out of 10 in 3oxm

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Thallium binding site 8 out of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 8 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl208

b:0.9
occ:0.20
 O6 B:G8 2.7 50.2 1.0
O4 B:U6 3.2 54.3 1.0
C6 B:G8 3.7 48.8 1.0
C4 B:U6 3.7 53.8 1.0
C5 B:U6 4.0 53.9 1.0
O6 B:G7 4.0 50.0 1.0
TL B:TL203 4.2 0.4 0.8
N1 B:G8 4.3 48.6 1.0
N7 B:G7 4.5 50.2 1.0
C5 B:G8 4.6 48.0 1.0
N3 B:U6 4.7 53.5 1.0
C6 B:G7 4.9 49.5 1.0
N7 B:G8 5.0 48.1 1.0
C6 B:U6 5.0 53.9 1.0

Thallium binding site 9 out of 10 in 3oxm

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Thallium binding site 9 out of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 9 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl209

b:0.5
occ:0.50
 O6 B:G1 3.2 88.5 1.0
O6 B:G2 3.4 83.4 1.0
N7 B:G2 3.6 82.4 1.0
C6 B:G1 3.8 88.4 1.0
C6 B:G2 4.1 83.3 1.0
O4 B:U87 4.1 79.6 1.0
C5 B:G2 4.2 83.0 1.0
N4 B:CCC88 4.3 85.5 1.0
C5 B:G1 4.3 88.1 1.0
N7 B:G1 4.3 87.7 1.0
N4 B:C3 4.5 72.1 1.0
O6 B:G86 4.7 69.4 1.0
N1 B:G1 4.7 88.6 1.0
C8 B:G2 4.8 82.5 1.0

Thallium binding site 10 out of 10 in 3oxm

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Thallium binding site 10 out of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 10 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl210

b:0.5
occ:0.30
 OP2 A:A78 2.4 62.5 1.0
P A:A78 3.8 62.5 1.0
N7 A:G79 3.9 58.5 1.0
O6 A:G79 4.0 57.0 1.0
O6 A:G80 4.0 62.3 1.0
N7 A:A78 4.0 60.1 1.0
O5' A:A78 4.1 62.1 1.0
C8 A:A78 4.3 60.6 1.0
OP2 A:A77 4.5 62.1 1.0
OP1 A:A77 4.5 63.5 1.0
O5' A:A77 4.6 62.6 1.0
OP1 A:A78 4.7 63.4 1.0
C5 A:G79 4.7 57.9 1.0
C6 A:G79 4.7 57.5 1.0
C6 A:G80 4.7 61.5 1.0
P A:A77 4.7 62.9 1.0
O3' A:A77 4.8 62.3 1.0
C8 A:G79 4.9 58.9 1.0
C3' A:A77 4.9 62.1 1.0

Reference:

L.Huang, A.Serganov, D.J.Patel. Structural Insights Into Ligand Recognition By A Sensing Domain of the Cooperative Glycine Riboswitch. Mol.Cell V. 40 774 2010.
ISSN: ISSN 1097-2765
PubMed: 21145485
DOI: 10.1016/J.MOLCEL.2010.11.026
Page generated: Fri Oct 11 09:51:12 2024

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