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Thallium in PDB 4e8q: Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+

Protein crystallography data

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+, PDB code: 4e8q was solved by M.Marcia, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.51 / 2.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.459, 95.680, 225.144, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.2

Other elements in 4e8q:

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ also contains other interesting chemical elements:

Magnesium (Mg) 30 atoms

Thallium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Thallium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ (pdb code 4e8q). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 17 binding sites of Thallium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+, PDB code: 4e8q:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Thallium binding site 1 out of 17 in 4e8q

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Thallium binding site 1 out of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl401

b:0.1
occ:0.41
O6 A:G15 3.4 86.3 1.0
O6 A:G14 3.9 93.2 1.0
N7 A:G15 4.0 81.8 1.0
C6 A:G15 4.3 86.3 1.0
N7 A:G14 4.4 69.3 1.0
O2' A:A12 4.5 86.9 1.0
OP2 A:U13 4.5 0.2 1.0
C6 A:G14 4.5 76.4 1.0
C5 A:G15 4.5 84.5 1.0
C2' A:A12 4.5 87.4 1.0
O4 A:U256 4.6 0.9 1.0
C5 A:G14 4.7 70.1 1.0
C3' A:A12 4.9 92.0 1.0

Thallium binding site 2 out of 17 in 4e8q

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Thallium binding site 2 out of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl402

b:0.8
occ:0.28
O A:HOH512 2.2 67.8 1.0
O A:HOH517 2.4 63.0 1.0
OP2 A:G269 2.5 73.8 1.0
N7 A:G270 3.4 79.5 1.0
N7 A:G269 3.5 79.9 1.0
OP2 A:A268 3.5 76.8 1.0
O5' A:A268 3.6 75.3 1.0
O6 A:G270 3.6 81.0 1.0
P A:G269 3.8 82.7 1.0
C8 A:G269 3.9 81.4 1.0
O5' A:G269 4.0 81.6 1.0
C5 A:G270 4.2 78.3 1.0
C6 A:G270 4.2 79.8 1.0
P A:A268 4.3 78.0 1.0
C3' A:A268 4.4 83.8 1.0
C8 A:G270 4.5 83.0 1.0
N2 A:G284 4.6 67.3 1.0
O3' A:A268 4.6 84.0 1.0
C5 A:G269 4.6 78.2 1.0
C5' A:A268 4.6 84.0 1.0
O4 A:U271 4.9 79.7 1.0
OP2 A:G270 5.0 94.6 1.0

Thallium binding site 3 out of 17 in 4e8q

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Thallium binding site 3 out of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl403

b:98.1
occ:0.29
O A:HOH508 2.3 49.9 1.0
O A:HOH523 2.7 63.5 1.0
O6 A:G266 2.8 67.1 1.0
N7 A:G267 3.0 67.1 1.0
C6 A:G266 3.4 67.2 1.0
N7 A:G266 3.6 74.2 1.0
C5 A:G266 3.7 68.4 1.0
O6 A:G267 3.8 65.0 1.0
C5 A:G267 3.9 71.2 1.0
C8 A:G267 4.0 71.0 1.0
C6 A:G267 4.2 69.8 1.0
N1 A:G266 4.4 65.6 1.0
C8 A:G266 4.7 76.4 1.0
C4 A:G266 4.9 70.2 1.0

Thallium binding site 4 out of 17 in 4e8q

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Thallium binding site 4 out of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl404

b:98.0
occ:0.47
O A:HOH518 2.0 49.0 1.0
O6 A:G320 3.0 95.4 1.0
N1 A:A297 3.1 97.8 1.0
N7 A:G320 3.1 93.0 1.0
O6 A:G321 3.4 0.9 1.0
C2 A:A297 3.6 0.3 1.0
C6 A:G320 3.6 92.3 1.0
C5 A:G320 3.7 90.4 1.0
OP2 A:G320 3.9 94.7 1.0
C6 A:A297 4.2 0.1 1.0
C6 A:G321 4.2 0.4 1.0
C8 A:G320 4.3 85.7 1.0
N6 A:A297 4.4 0.4 1.0
OP2 A:A319 4.5 94.1 1.0
N7 A:G321 4.6 0.8 1.0
O4 A:U298 4.7 93.1 1.0
C5 A:G321 4.7 98.7 1.0
N3 A:A297 4.9 0.7 1.0
O5' A:A319 4.9 90.0 1.0
N1 A:G320 5.0 84.2 1.0

Thallium binding site 5 out of 17 in 4e8q

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Thallium binding site 5 out of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl405

b:82.4
occ:0.24
N7 A:G170 2.5 59.7 1.0
O A:HOH507 2.8 63.6 1.0
O A:HOH536 2.9 69.3 1.0
O6 A:G170 2.9 54.8 1.0
C5 A:G170 3.3 56.7 1.0
C6 A:G170 3.4 54.8 1.0
C8 A:G170 3.7 60.9 1.0
N7 A:G169 3.8 56.3 1.0
O6 A:G169 4.0 56.5 1.0
C5 A:G169 4.2 53.5 1.0
N7 A:A171 4.2 61.7 1.0
N6 A:A171 4.2 63.0 1.0
C6 A:G169 4.3 53.9 1.0
C4 A:G170 4.6 55.6 1.0
C8 A:G169 4.6 56.9 1.0
N9 A:G170 4.7 58.5 1.0
N1 A:G170 4.8 53.7 1.0
C5 A:A171 4.9 57.1 1.0
C6 A:A171 5.0 57.8 1.0

Thallium binding site 6 out of 17 in 4e8q

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Thallium binding site 6 out of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl406

b:90.0
occ:0.30
N3 A:C377 2.7 87.8 1.0
O2 A:C377 3.2 76.7 1.0
C2 A:C377 3.3 83.7 1.0
O A:HOH524 3.3 59.4 1.0
O6 A:G382 3.4 0.7 1.0
N4 A:C381 3.7 91.8 1.0
C4 A:C377 3.7 89.2 1.0
N4 A:C377 3.9 93.6 1.0
N4 A:C361 4.1 92.3 1.0
N4 A:C360 4.3 0.6 1.0
C6 A:G382 4.5 0.9 1.0
N1 A:C377 4.6 84.5 1.0
O6 A:G383 4.6 0.2 1.0
MG A:MG444 4.7 82.0 1.0
C4 A:C381 4.9 0.6 1.0
C5 A:C377 4.9 89.4 1.0

Thallium binding site 7 out of 17 in 4e8q

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Thallium binding site 7 out of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl407

b:82.5
occ:0.30
O A:HOH503 2.4 54.4 1.0
O4 A:U4 2.7 76.1 1.0
OP2 A:A376 3.1 69.8 1.0
O2' A:U375 3.3 67.2 1.0
O3' A:U375 3.3 76.3 1.0
O6 A:G107 3.4 67.1 1.0
C4 A:U4 3.7 71.1 1.0
P A:A376 4.0 75.5 1.0
N3 A:U4 4.0 64.4 1.0
N7 A:A106 4.2 72.1 1.0
C3' A:U375 4.3 72.1 1.0
C2' A:U375 4.4 67.8 1.0
O6 A:G3 4.4 73.5 1.0
TL A:TL415 4.4 0.8 0.2
C6 A:G107 4.5 69.8 1.0
C8 A:A106 4.5 74.8 1.0
N7 A:G107 4.7 78.6 1.0
C4' A:U375 4.8 66.3 1.0
O2' A:G1 4.8 0.8 1.0
N1 A:G5 4.8 66.7 1.0
OP1 A:A376 4.9 64.2 1.0
N7 A:G3 5.0 73.2 1.0

Thallium binding site 8 out of 17 in 4e8q

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Thallium binding site 8 out of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl408

b:0.7
occ:0.40
O6 A:G275 3.2 90.2 1.0
N7 A:G275 3.2 83.0 1.0
C6 A:G275 3.8 82.1 1.0
C5 A:G275 3.8 81.2 1.0
C8 A:G275 4.3 82.5 1.0
OP2 A:A277 4.4 78.9 1.0
OP1 A:A277 4.6 84.1 1.0
O A:HOH547 4.7 67.0 1.0

Thallium binding site 9 out of 17 in 4e8q

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Thallium binding site 9 out of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 9 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl409

b:60.6
occ:0.21
O A:HOH538 2.6 37.4 1.0
O6 A:G87 2.7 64.9 1.0
O4 A:U96 3.2 71.1 1.0
O6 A:G97 3.2 56.0 1.0
N6 A:A95 3.3 62.9 1.0
N4 A:C86 3.3 68.0 1.0
O4 A:U88 3.7 69.3 1.0
C6 A:G87 3.7 65.3 1.0
C4 A:U96 4.0 64.2 1.0
N3 A:U96 4.1 60.0 1.0
C6 A:G97 4.1 55.0 1.0
N7 A:G87 4.1 70.2 1.0
C4 A:C86 4.2 68.4 1.0
C5 A:G87 4.3 67.3 1.0
C6 A:A95 4.3 62.3 1.0
C4 A:U88 4.4 68.8 1.0
N1 A:G97 4.6 55.7 1.0
N1 A:A95 4.8 62.9 1.0
C5 A:C86 4.8 70.8 1.0
O A:HOH537 4.8 62.3 1.0
N3 A:C86 4.9 67.2 1.0
N1 A:G87 4.9 63.6 1.0
N3 A:U88 5.0 67.8 1.0

Thallium binding site 10 out of 17 in 4e8q

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Thallium binding site 10 out of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 10 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl410

b:83.9
occ:0.30
O2' A:G32 2.9 83.4 1.0
O6 A:G34 3.0 68.3 1.0
N7 A:A33 3.2 73.5 1.0
C6 A:G34 3.9 68.0 1.0
C8 A:A33 4.1 72.8 1.0
N6 A:A33 4.2 79.2 1.0
O3' A:G32 4.2 92.5 1.0
C5 A:A33 4.3 73.3 1.0
C2' A:G32 4.3 82.1 1.0
N7 A:G34 4.5 69.5 1.0
C5 A:G34 4.5 69.0 1.0
C6 A:A33 4.7 75.9 1.0
C3' A:G32 4.7 89.7 1.0
C4' A:G32 4.7 89.4 1.0
N1 A:G34 4.9 68.7 1.0

Reference:

M.Marcia, A.M.Pyle. Visualizing Group II Intron Catalysis Through the Stages of Splicing. Cell(Cambridge,Mass.) V. 151 497 2012.
ISSN: ISSN 0092-8674
PubMed: 23101623
DOI: 10.1016/J.CELL.2012.09.033
Page generated: Wed Dec 16 02:28:46 2020

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