Magnesium in PDB 8tjv: Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch

Other elements in 8tjv:

The structure of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch also contains other interesting chemical elements:

Potassium (K) 1 atom
Fluorine (F) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Magnesium atom in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch (pdb code 8tjv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 30 binding sites of Magnesium where determined in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch, PDB code: 8tjv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 30 in 8tjv

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Magnesium binding site 1 out of 30 in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:306.4
occ:1.00
 MG A:MG503 1.6 305.8 1.0
F A:F504 1.7 307.3 1.0
OP1 A:U7 2.1 298.3 1.0
OP1 A:A6 2.6 285.4 1.0
OP2 A:U7 2.8 298.3 1.0
P A:U7 2.8 298.3 1.0
MG A:MG502 2.9 305.4 1.0
OP2 A:G8 3.3 314.6 1.0
OP2 A:G407 3.4 315.2 1.0
OP1 A:U406 3.6 311.8 1.0
P A:A6 3.7 285.4 1.0
OP1 A:G8 3.9 314.6 1.0
OP2 A:A6 3.9 285.4 1.0
K A:K505 4.0 301.9 1.0
O5' A:U7 4.0 298.3 1.0
O3' A:A6 4.0 285.4 1.0
P A:G8 4.1 314.6 1.0
P A:G407 4.1 315.2 1.0
OP1 A:G407 4.2 315.2 1.0
C5' A:U406 4.2 311.8 1.0
O5' A:A6 4.3 285.4 1.0
O3' A:U406 4.6 311.8 1.0
P A:U406 4.8 311.8 1.0
O5' A:G5 4.9 315.1 1.0
C3' A:A6 5.0 285.4 1.0
O2' A:A405 5.0 308.7 1.0

Magnesium binding site 2 out of 30 in 8tjv

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Magnesium binding site 2 out of 30 in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:305.4
occ:1.00
 MG A:MG503 1.5 305.8 1.0
OP2 A:U7 2.0 298.3 1.0
OP2 A:G407 2.0 315.2 1.0
F A:F504 2.0 307.3 1.0
OP1 A:U406 2.0 311.8 1.0
OP2 A:A6 2.0 285.4 1.0
MG A:MG501 2.9 306.4 1.0
P A:A6 3.0 285.4 1.0
OP1 A:A6 3.2 285.4 1.0
P A:U7 3.3 298.3 1.0
P A:U406 3.3 311.8 1.0
P A:G407 3.4 315.2 1.0
O5' A:A6 3.8 285.4 1.0
OP1 A:U7 3.9 298.3 1.0
O5' A:U406 4.0 311.8 1.0
C5' A:U406 4.0 311.8 1.0
OP2 A:U406 4.0 311.8 1.0
OP1 A:G407 4.1 315.2 1.0
O3' A:A6 4.2 285.4 1.0
C3' A:A6 4.2 285.4 1.0
O5' A:G407 4.3 315.2 1.0
O3' A:G5 4.3 315.1 1.0
C5' A:A6 4.3 285.4 1.0
O3' A:U406 4.3 311.8 1.0
O5' A:U7 4.4 298.3 1.0
C5' A:G407 4.4 315.2 1.0
N2 A:G404 4.5 284.9 1.0
O3' A:A405 4.5 308.7 1.0
C3' A:U406 4.6 311.8 1.0
C4' A:U406 4.9 311.8 1.0
C4' A:A6 4.9 285.4 1.0

Magnesium binding site 3 out of 30 in 8tjv

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Magnesium binding site 3 out of 30 in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:305.8
occ:1.00
 MG A:MG502 1.5 305.4 1.0
MG A:MG501 1.6 306.4 1.0
F A:F504 1.7 307.3 1.0
OP1 A:A6 2.0 285.4 1.0
OP2 A:G407 2.1 315.2 1.0
OP2 A:U7 2.3 298.3 1.0
OP2 A:A6 2.4 285.4 1.0
P A:A6 2.5 285.4 1.0
OP1 A:U406 2.9 311.8 1.0
P A:U7 3.1 298.3 1.0
OP1 A:U7 3.1 298.3 1.0
P A:G407 3.1 315.2 1.0
OP1 A:G407 3.4 315.2 1.0
O5' A:A6 3.5 285.4 1.0
O3' A:G5 3.9 315.1 1.0
O3' A:U406 3.9 311.8 1.0
O3' A:A6 4.0 285.4 1.0
C5' A:U406 4.0 311.8 1.0
P A:U406 4.3 311.8 1.0
K A:K505 4.3 301.9 1.0
O5' A:G407 4.4 315.2 1.0
O5' A:U7 4.4 298.3 1.0
C5' A:A6 4.5 285.4 1.0
C3' A:A6 4.5 285.4 1.0
O5' A:U406 4.5 311.8 1.0
OP2 A:G8 4.5 314.6 1.0
C3' A:G5 4.6 315.1 1.0
C3' A:U406 4.6 311.8 1.0
C5' A:G407 4.7 315.2 1.0
C4' A:U406 4.8 311.8 1.0

Magnesium binding site 4 out of 30 in 8tjv

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Magnesium binding site 4 out of 30 in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:51.8
occ:0.77
 O6 A:G280 4.0 62.9 1.0
O6 A:G279 4.2 57.0 1.0
N7 A:G280 4.3 62.9 1.0
N7 A:G279 4.7 57.0 1.0
C6 A:G279 4.7 57.0 1.0
O6 A:G281 4.8 73.8 1.0
C6 A:G280 4.8 62.9 1.0
C5 A:G279 4.9 57.0 1.0
C5 A:G280 5.0 62.9 1.0

Magnesium binding site 5 out of 30 in 8tjv

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Magnesium binding site 5 out of 30 in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:78.7
occ:1.00
 OP1 A:A376 2.0 92.4 1.0
OP2 A:C45 2.2 62.9 1.0
P A:C45 3.3 62.9 1.0
P A:A376 3.4 92.4 1.0
OP1 A:C45 3.6 62.9 1.0
OP2 A:A376 4.1 92.4 1.0
O3' A:A44 4.3 54.1 1.0
O5' A:A376 4.3 92.4 1.0
O3' A:A375 4.3 91.1 1.0
C3' A:A44 4.3 54.1 1.0
C5' A:A376 4.4 92.4 1.0
O5' A:C45 4.4 62.9 1.0
C5' A:C45 4.7 62.9 1.0
O2 A:U88 4.9 54.6 1.0
O2' A:U88 4.9 54.6 1.0

Magnesium binding site 6 out of 30 in 8tjv

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Magnesium binding site 6 out of 30 in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:87.9
occ:0.87
 O6 A:G285 3.9 99.7 1.0
OP2 A:A283 4.2 95.0 1.0
N7 A:A284 4.3 98.4 1.0
N7 A:G285 4.4 99.7 1.0
OP2 A:A284 4.4 98.4 1.0
O6 A:G286 4.4 96.7 1.0
O4 A:U374 4.5 91.3 1.0
C6 A:G285 4.8 99.7 1.0
C5 A:G285 5.0 99.7 1.0
N6 A:A284 5.0 98.4 1.0

Magnesium binding site 7 out of 30 in 8tjv

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Magnesium binding site 7 out of 30 in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg509

b:59.9
occ:0.78
 OP1 A:A353 1.9 55.1 1.0
OP1 A:A355 2.0 58.1 1.0
OP2 A:A356 2.0 65.0 1.0
OP2 A:G357 2.2 57.0 1.0
P A:A355 3.3 58.1 1.0
P A:A353 3.3 55.1 1.0
P A:A356 3.4 65.0 1.0
P A:G357 3.6 57.0 1.0
C5' A:A356 3.9 65.0 1.0
OP2 A:A355 3.9 58.1 1.0
OP2 A:A353 4.0 55.1 1.0
OP1 A:G357 4.1 57.0 1.0
O3' A:A352 4.1 53.8 1.0
OP1 A:A356 4.1 65.0 1.0
O5' A:A355 4.1 58.1 1.0
O5' A:A356 4.2 65.0 1.0
C3' A:A355 4.3 58.1 1.0
O5' A:A353 4.4 55.1 1.0
O3' A:A355 4.4 58.1 1.0
O3' A:U354 4.4 61.6 1.0
O5' A:G357 4.5 57.0 1.0
C5' A:A355 4.5 58.1 1.0
OP1 A:A352 4.6 53.8 1.0
O3' A:A356 4.6 65.0 1.0
C4' A:A356 4.7 65.0 1.0
C3' A:U354 4.9 61.6 1.0
C5' A:A352 4.9 53.8 1.0
C4' A:U354 4.9 61.6 1.0
C5' A:A353 5.0 55.1 1.0

Magnesium binding site 8 out of 30 in 8tjv

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Magnesium binding site 8 out of 30 in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg510

b:52.4
occ:0.85
 OP1 A:A352 2.0 53.8 1.0
OP2 A:A353 2.2 55.1 1.0
OP2 A:A355 2.5 58.1 1.0
P A:A352 3.3 53.8 1.0
P A:A353 3.6 55.1 1.0
P A:A355 3.9 58.1 1.0
OP2 A:A352 3.9 53.8 1.0
O5' A:A352 4.0 53.8 1.0
N7 A:A353 4.2 55.1 1.0
OP1 A:A353 4.3 55.1 1.0
C3' A:A352 4.3 53.8 1.0
O3' A:U351 4.5 58.8 1.0
N7 A:A355 4.5 58.1 1.0
O3' A:A352 4.5 53.8 1.0
C8 A:A353 4.6 55.1 1.0
OP1 A:A355 4.6 58.1 1.0
O5' A:A353 4.6 55.1 1.0
C5' A:A352 4.7 53.8 1.0
C8 A:A355 4.7 58.1 1.0
O5' A:A355 4.7 58.1 1.0
O3' A:U354 4.8 61.6 1.0
C3' A:U354 4.9 61.6 1.0
C2 A:A308 4.9 61.1 1.0
N3 A:A308 5.0 61.1 1.0

Magnesium binding site 9 out of 30 in 8tjv

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Magnesium binding site 9 out of 30 in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg511

b:46.2
occ:0.81
 O6 A:G357 2.3 57.0 1.0
C6 A:G357 3.2 57.0 1.0
N7 A:G357 3.6 57.0 1.0
C5 A:G357 3.7 57.0 1.0
OP1 A:U337 4.2 61.0 1.0
N7 A:A352 4.3 53.8 1.0
N1 A:G357 4.4 57.0 1.0
OP2 A:A352 4.4 53.8 1.0
C8 A:A352 4.4 53.8 1.0
OP1 A:C334 4.4 61.4 1.0
OP1 A:C335 4.6 62.4 1.0
OP2 A:U337 4.7 61.0 1.0
OP1 A:U351 4.7 58.8 1.0
OP2 A:C335 4.7 62.4 1.0
C8 A:G357 4.8 57.0 1.0
C5 A:U337 4.8 61.0 1.0
P A:U337 5.0 61.0 1.0

Magnesium binding site 10 out of 30 in 8tjv

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Magnesium binding site 10 out of 30 in the Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Tetrahymena Ribozyme Scaffolded Fluoride Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg512

b:61.3
occ:0.84
 O6 A:G333 2.1 63.0 1.0
N7 A:G332 2.2 67.4 1.0
C8 A:G332 3.0 67.4 1.0
C6 A:G333 3.1 63.0 1.0
C5 A:G332 3.2 67.4 1.0
O6 A:G332 3.7 67.4 1.0
C5 A:G333 3.8 63.0 1.0
C6 A:G332 3.8 67.4 1.0
N7 A:G333 3.9 63.0 1.0
OP2 A:G332 4.0 67.4 1.0
N1 A:G333 4.1 63.0 1.0
N9 A:G332 4.2 67.4 1.0
C4 A:G332 4.3 67.4 1.0
C5 A:U331 4.8 75.7 1.0
N6 A:A347 4.8 73.2 1.0
OP2 A:U331 4.8 75.7 1.0
N7 A:A347 4.8 73.2 1.0
O5' A:G332 4.9 67.4 1.0
C6 A:U331 4.9 75.7 1.0

Reference:

C.J.Langeberg, J.S.Kieft. A Generalizable Scaffold-Based Approach For Structure Determination of Rnas By Cryo-Em. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37791881
DOI: 10.1093/NAR/GKAD784
Page generated: Fri Oct 4 20:43:07 2024

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