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Caesium in PDB 4jf2: Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold

Protein crystallography data

The structure of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold, PDB code: 4jf2 was solved by J.A.Liberman, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.70 / 2.28
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 58.036, 85.972, 98.120, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.4

Other elements in 4jf2:

The structure of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Caesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Caesium atom in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold (pdb code 4jf2). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 15 binding sites of Caesium where determined in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold, PDB code: 4jf2:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Caesium binding site 1 out of 15 in 4jf2

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Caesium binding site 1 out of 15 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


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Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs102

b:20.5
occ:0.82
N7 A:A10 3.2 16.1 1.0
O3' A:G9 3.2 19.0 1.0
O A:HOH263 3.3 22.9 1.0
O A:HOH332 3.4 13.7 1.0
OP1 A:A10 3.4 23.4 1.0
C8 A:A10 3.7 16.6 1.0
O A:HOH334 3.8 38.6 1.0
P A:A10 4.0 20.3 1.0
O2' A:G9 4.2 28.0 1.0
MG A:MG120 4.3 30.8 1.0
C3' A:G9 4.3 19.6 1.0
C4' A:G9 4.4 21.4 1.0
C5 A:A10 4.5 15.3 1.0
C2' A:G9 4.9 19.2 1.0

Caesium binding site 2 out of 15 in 4jf2

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Caesium binding site 2 out of 15 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


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Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs103

b:27.4
occ:0.56
OP2 A:A52 3.0 40.0 1.0
O5' A:G65 3.1 31.9 1.0
O4 A:U53 3.1 28.3 1.0
O3' A:U51 3.3 42.8 1.0
P A:A52 3.6 41.2 1.0
O2' A:G64 3.6 54.8 1.0
O2' A:U51 3.8 38.4 1.0
C4 A:U53 3.9 25.6 1.0
C5 A:U53 4.0 25.1 1.0
P A:G65 4.0 63.6 1.0
O3' A:G64 4.0 54.6 1.0
C5' A:G65 4.1 38.0 1.0
OP1 A:G65 4.1 61.1 1.0
OP1 A:A52 4.2 43.6 1.0
O A:HOH214 4.3 24.3 1.0
C3' A:U51 4.4 40.1 1.0
C2' A:G64 4.6 55.3 1.0
C2' A:U51 4.7 39.8 1.0
C4' A:G65 4.8 45.3 1.0
C3' A:G64 4.9 55.2 1.0

Caesium binding site 3 out of 15 in 4jf2

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Caesium binding site 3 out of 15 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


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Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs104

b:64.6
occ:0.53
O A:HOH348 2.5 7.5 1.0
O A:HOH349 3.1 13.0 1.0
O6 A:G58 3.1 21.4 1.0
O6 A:G59 3.3 25.2 1.0
O A:HOH350 3.9 44.3 1.0
O4 A:U57 4.2 13.8 1.0
C6 A:G58 4.2 18.4 1.0
N4 A:C66 4.2 19.6 1.0
N4 A:C67 4.3 15.9 1.0
C6 A:G59 4.3 27.0 1.0
OP2 A:C56 4.4 14.8 1.0
N7 A:G58 4.6 15.4 1.0
O2' A:U54 4.7 28.4 1.0
C5 A:G58 4.7 19.2 1.0
O A:HOH279 4.9 33.4 1.0
C4 A:U57 4.9 17.2 1.0
O2 A:U54 4.9 46.0 1.0
N7 A:G59 4.9 31.3 1.0
C5 A:G59 5.0 28.8 1.0

Caesium binding site 4 out of 15 in 4jf2

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Caesium binding site 4 out of 15 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


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Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs105

b:49.0
occ:0.50
O2 A:C5 3.1 33.5 1.0
O2' A:C5 3.1 37.7 1.0
O2 A:U17 3.3 40.7 1.0
O4' A:C6 3.6 36.2 1.0
N2 A:G16 3.7 25.0 1.0
C2' A:C5 3.9 34.7 1.0
C1' A:C5 4.0 31.8 1.0
C2 A:U17 4.2 39.0 1.0
C2 A:C5 4.3 32.5 1.0
C1' A:C6 4.4 35.7 1.0
C4' A:C6 4.7 35.8 1.0
N1 A:C5 4.7 32.1 1.0
C1' A:U17 4.8 35.5 1.0
N1 A:C6 4.9 35.1 1.0
N1 A:U17 4.9 36.0 1.0
N3 A:U17 4.9 36.2 1.0
C5' A:C6 5.0 33.8 1.0

Caesium binding site 5 out of 15 in 4jf2

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Caesium binding site 5 out of 15 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


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Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs106

b:18.3
occ:0.38
O2' A:C48 3.0 36.0 1.0
O2 A:C48 3.3 16.1 1.0
O4' A:G49 3.5 27.4 1.0
C2' A:C48 3.8 17.4 1.0
C1' A:G49 3.9 23.8 1.0
O A:HOH345 3.9 41.1 1.0
O A:HOH255 3.9 31.6 1.0
O2' A:G49 4.1 29.2 1.0
C1' A:C48 4.1 16.6 1.0
N2 A:G23 4.2 20.3 1.0
C4' A:G49 4.2 25.7 1.0
C2 A:C48 4.4 22.2 1.0
C2' A:G49 4.6 26.6 1.0
O A:HOH248 4.7 17.8 1.0
O A:HOH347 4.7 18.4 1.0
N1 A:C48 4.8 16.4 1.0
O5' A:G49 5.0 19.6 1.0

Caesium binding site 6 out of 15 in 4jf2

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Caesium binding site 6 out of 15 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs107

b:52.7
occ:0.53
O4 A:U53 3.1 28.3 1.0
O2 A:U51 3.2 40.9 1.0
O2' A:U51 3.5 38.4 1.0
O3' A:G65 3.9 51.8 1.0
C2 A:U51 3.9 40.3 1.0
C4 A:U53 3.9 25.6 1.0
OP1 A:C66 4.0 62.8 1.0
N3 A:U53 4.2 26.2 1.0
N3 A:U51 4.6 36.5 1.0
N1 A:U51 4.6 40.5 1.0
P A:C66 4.7 60.3 1.0
C2' A:U51 4.7 39.8 1.0
C1' A:U51 4.7 39.3 1.0
C4' A:G65 4.7 45.3 1.0
C3' A:G65 4.8 48.0 1.0
O2' A:G65 4.9 46.5 1.0

Caesium binding site 7 out of 15 in 4jf2

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Caesium binding site 7 out of 15 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs108

b:41.6
occ:0.41
O1G A:GTP1 3.1 60.3 0.5
O3B A:GTP1 3.4 67.2 1.0
O A:HOH265 3.5 21.0 1.0
PG A:GTP1 3.7 59.6 0.5
O1B A:GTP1 3.7 95.2 1.0
O A:HOH286 4.0 34.9 1.0
O3G A:GTP1 4.0 58.1 0.5
O A:HOH236 4.2 49.7 1.0
PB A:GTP1 4.2 95.5 1.0
CS A:CS115 4.5 47.4 0.3
O2A A:GTP1 4.6 50.4 1.0
OP2 A:U50 5.0 29.8 1.0

Caesium binding site 8 out of 15 in 4jf2

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Caesium binding site 8 out of 15 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 8 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs109

b:17.0
occ:0.36
O A:HOH347 2.8 18.4 1.0
O A:HOH346 3.1 66.1 1.0
O A:HOH345 3.2 41.1 1.0
O2' A:A24 3.2 23.6 1.0
O2' A:A52 3.4 41.5 1.0
O4' A:A24 3.5 15.7 1.0
C4' A:A24 3.8 17.1 1.0
C1' A:A24 3.9 13.4 1.0
C2' A:A24 4.1 19.1 1.0
C3' A:A24 4.6 16.4 1.0
O A:HOH230 4.7 11.8 1.0
C2' A:A52 4.7 44.4 1.0
O A:HOH266 4.7 14.5 1.0
C5' A:A24 4.8 15.5 1.0

Caesium binding site 9 out of 15 in 4jf2

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Caesium binding site 9 out of 15 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 9 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs110

b:53.7
occ:0.33
O2 A:C6 3.0 35.9 1.0
O2' A:C6 3.2 37.7 1.0
O4' A:G7 3.5 29.1 1.0
C2' A:C6 3.8 35.2 1.0
N2 A:G15 3.8 24.2 1.0
C1' A:C6 4.0 35.7 1.0
C2 A:C6 4.1 36.8 1.0
C1' A:G7 4.2 28.1 1.0
C4' A:G7 4.5 32.8 1.0
N1 A:C6 4.6 35.1 1.0
N9 A:G7 4.8 28.5 1.0

Caesium binding site 10 out of 15 in 4jf2

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Caesium binding site 10 out of 15 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 10 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs111

b:31.5
occ:0.32
O2 A:C66 2.9 29.0 1.0
O A:HOH303 3.1 22.7 1.0
O2' A:C66 3.2 32.6 1.0
O4' A:C67 3.5 26.6 1.0
C2' A:C66 3.8 34.0 1.0
N2 A:G59 3.8 20.2 1.0
C1' A:C66 3.8 34.0 1.0
O2 A:C60 3.8 32.3 1.0
C2 A:C66 4.0 29.1 1.0
C1' A:C67 4.2 28.2 1.0
N2 A:G65 4.4 28.8 1.0
N1 A:C66 4.4 33.4 1.0
C4' A:C67 4.6 27.0 1.0
N1 A:C67 4.7 23.6 1.0
C2 A:C60 4.8 34.6 1.0
C1' A:C60 4.9 38.7 1.0
O2' A:C60 4.9 45.5 1.0

Reference:

J.A.Liberman, M.Salim, J.Krucinska, J.E.Wedekind. Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold. Nat.Chem.Biol. V. 9 353 2013.
ISSN: ISSN 1552-4450
PubMed: 23584677
DOI: 10.1038/NCHEMBIO.1231
Page generated: Sun Dec 13 10:56:26 2020

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