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Caesium in PDB 5d5l: PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+

Protein crystallography data

The structure of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+, PDB code: 5d5l was solved by J.E.Wedekind, J.A.Liberman, M.Salim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.37 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.358, 57.833, 99.493, 90.00, 107.64, 90.00
R / Rfree (%) 19.9 / 24.7

Other elements in 5d5l:

The structure of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ also contains other interesting chemical elements:

Magnesium (Mg) 15 atoms

Caesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Caesium atom in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ (pdb code 5d5l). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 32 binding sites of Caesium where determined in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+, PDB code: 5d5l:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Caesium binding site 1 out of 32 in 5d5l

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Caesium binding site 1 out of 32 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs101

b:87.9
occ:0.50
O3A A:GTP1 3.2 94.7 1.0
O2A A:GTP1 3.3 78.0 1.0
O1G A:GTP1 3.4 99.4 1.0
OP2 A:G2 3.5 64.2 1.0
O A:HOH231 3.7 40.7 1.0
PA A:GTP1 3.8 66.5 1.0
O A:HOH227 3.9 55.7 1.0
O A:HOH206 3.9 42.5 1.0
C5' A:GTP1 4.2 60.4 1.0
PB A:GTP1 4.3 72.5 1.0
H3' A:GTP1 4.3 67.9 1.0
PG A:GTP1 4.4 95.6 1.0
P A:G2 4.4 61.4 1.0
O3B A:GTP1 4.5 77.8 1.0
O5' A:GTP1 4.5 60.7 1.0
O2B A:GTP1 4.5 67.2 1.0
OP1 A:G2 4.5 59.9 1.0
O3G A:GTP1 4.6 98.0 1.0
O3' A:GTP1 4.7 58.9 1.0
C3' A:GTP1 4.9 56.6 1.0

Caesium binding site 2 out of 32 in 5d5l

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Caesium binding site 2 out of 32 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs102

b:73.2
occ:1.00
O6 A:G6 3.1 52.7 1.0
O4 A:U15 3.3 61.9 1.0
O6 A:G14 3.4 48.8 1.0
O6 A:G5 3.5 52.7 1.0
H42 A:C7 3.6 66.3 1.0
H3 A:U15 3.8 64.6 1.0
H42 A:C16 3.8 63.5 1.0
N4 A:C7 4.0 55.3 1.0
H41 A:C7 4.0 66.3 1.0
O A:HOH203 4.0 57.3 1.0
C6 A:G6 4.2 53.5 1.0
C6 A:G5 4.2 53.8 1.0
C4 A:U15 4.3 56.4 1.0
N4 A:C16 4.3 52.9 1.0
N3 A:U15 4.4 53.8 1.0
C6 A:G14 4.4 48.8 1.0
N7 A:G6 4.5 57.8 1.0
H41 A:C16 4.6 63.5 1.0
C5 A:G6 4.7 57.0 1.0
C5 A:G5 4.9 58.5 1.0
H1 A:G5 4.9 65.0 1.0
N1 A:G5 4.9 54.2 1.0
H1 A:G14 4.9 64.2 1.0
C4 A:C7 4.9 55.4 1.0

Caesium binding site 3 out of 32 in 5d5l

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Caesium binding site 3 out of 32 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs103

b:62.5
occ:0.25
O A:HOH255 2.8 42.9 1.0
HO2' A:C16 3.1 78.2 1.0
O2' A:C16 3.4 65.2 1.0
O2 A:C16 3.4 60.0 1.0
H22 A:G6 3.5 67.6 1.0
H1' A:C16 3.7 78.4 1.0
H22 A:G5 3.8 74.2 1.0
H21 A:G5 3.8 74.2 1.0
N3 A:G6 3.8 58.0 1.0
O4' A:U17 3.8 68.6 1.0
N2 A:G6 3.9 56.4 1.0
H1' A:U17 3.9 73.8 1.0
H1' A:G6 4.1 75.7 1.0
C2 A:G6 4.1 55.6 1.0
N2 A:G5 4.1 61.9 1.0
C2' A:C16 4.2 62.7 1.0
H2' A:C16 4.2 75.2 1.0
C1' A:U17 4.4 61.5 1.0
C1' A:C16 4.4 65.3 1.0
H21 A:G6 4.5 67.6 1.0
C2 A:C16 4.6 54.4 1.0
C4 A:G6 4.6 61.0 1.0
H4' A:U17 4.8 80.2 1.0
H5' A:U17 4.8 77.9 1.0
C4' A:U17 4.9 66.8 1.0
C1' A:G6 4.9 63.1 1.0
N1 A:U17 5.0 57.9 1.0

Caesium binding site 4 out of 32 in 5d5l

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Caesium binding site 4 out of 32 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs104

b:85.3
occ:0.50
O A:HOH253 3.0 56.1 1.0
O2' A:U44 3.1 39.5 1.0
O2 A:U44 3.3 44.2 1.0
H1' A:U44 3.3 46.5 1.0
OP1 B:C8 3.4 60.6 1.0
O2 A:U28 3.5 55.4 1.0
O4' A:C45 3.6 42.7 1.0
O A:HOH205 3.7 52.9 1.0
C2' A:U44 3.8 38.6 1.0
H2' A:U44 3.8 46.3 1.0
H1' A:C45 3.9 44.9 1.0
H1' A:U28 4.0 59.6 1.0
C1' A:U44 4.0 38.8 1.0
O3' B:C7 4.2 45.8 1.0
C1' A:C45 4.3 37.5 1.0
P B:C8 4.3 51.9 1.0
H2 A:A27 4.3 41.2 1.0
C2 A:U44 4.3 41.6 1.0
HO2' A:U28 4.4 65.0 1.0
H5'' B:C7 4.5 53.7 1.0
C2 A:U28 4.5 50.1 1.0
H5' A:C45 4.6 53.9 1.0
N1 A:U44 4.7 36.5 1.0
H4' A:C45 4.7 47.9 1.0
C4' A:C45 4.7 39.9 1.0
H2 A:A43 4.7 43.8 1.0
N1 A:C45 4.8 35.5 1.0
OP2 B:C8 4.8 60.0 1.0
C1' A:U28 4.9 49.7 1.0
H6 A:C45 5.0 42.8 1.0

Caesium binding site 5 out of 32 in 5d5l

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Caesium binding site 5 out of 32 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs105

b:83.9
occ:1.00
N7 A:A10 3.3 56.9 1.0
O3' A:G9 3.3 52.6 1.0
H8 A:A10 3.5 65.3 1.0
OP1 A:A10 3.6 64.9 1.0
C8 A:A10 3.8 54.5 1.0
H4' A:G9 3.9 63.5 1.0
O2' A:G9 3.9 50.3 1.0
P A:A10 4.1 62.2 1.0
H62 A:A10 4.3 66.2 1.0
C3' A:G9 4.3 52.8 1.0
HO2' A:G9 4.4 60.4 1.0
C4' A:G9 4.6 52.9 1.0
C5 A:A10 4.6 50.4 1.0
C2' A:G9 4.8 51.7 1.0
H5'' A:G9 4.8 65.7 1.0

Caesium binding site 6 out of 32 in 5d5l

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Caesium binding site 6 out of 32 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs106

b:65.5
occ:0.75
OP2 A:A52 3.2 55.8 1.0
O2' A:G64 3.2 73.5 1.0
O5' A:G65 3.4 55.1 1.0
H5 A:U53 3.4 38.9 1.0
O4 A:U53 3.4 34.7 1.0
O3' A:U51 3.5 49.7 1.0
P A:A52 3.8 56.6 1.0
O3' A:G64 3.9 61.5 1.0
HO2' A:U51 3.9 65.2 1.0
O2' A:U51 3.9 54.4 1.0
C5 A:U53 4.0 32.5 1.0
C4 A:U53 4.1 33.2 1.0
P A:G65 4.2 54.9 1.0
C2' A:G64 4.2 68.3 1.0
OP1 A:A52 4.3 61.8 1.0
H4' A:G65 4.3 62.4 1.0
MG A:MG122 4.3 51.4 1.0
OP1 A:G65 4.4 58.8 1.0
H2' A:G64 4.4 82.0 1.0
H5' A:G65 4.4 61.9 1.0
C5' A:G65 4.4 51.6 1.0
C3' A:U51 4.6 52.6 1.0
C3' A:G64 4.6 65.4 1.0
C2' A:U51 4.8 49.6 1.0
H3' A:U51 4.8 63.1 1.0
C4' A:G65 4.9 52.0 1.0
H1' A:U51 4.9 61.2 1.0

Caesium binding site 7 out of 32 in 5d5l

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Caesium binding site 7 out of 32 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs107

b:84.5
occ:0.50
O4 A:U53 3.3 34.7 1.0
HO2' A:G65 3.5 83.8 1.0
HO2' A:U51 3.6 65.2 1.0
O3' A:G65 3.8 54.6 1.0
H4' A:G65 3.9 62.4 1.0
O2 A:U51 3.9 55.5 1.0
H3 A:U53 4.1 45.5 1.0
O2' A:U51 4.2 54.4 1.0
OP1 A:C66 4.3 74.0 1.0
O2' A:G65 4.3 69.8 1.0
C4 A:U53 4.3 33.2 1.0
C2 A:U51 4.4 56.6 1.0
H5' A:C66 4.4 57.3 1.0
N3 A:U53 4.6 37.9 1.0
C4' A:G65 4.7 52.0 1.0
C3' A:G65 4.7 55.2 1.0
H3 A:U51 4.7 67.9 1.0
P A:C66 4.7 61.8 1.0
N3 A:U51 4.8 56.6 1.0
H1' A:U51 4.9 61.2 1.0

Caesium binding site 8 out of 32 in 5d5l

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Caesium binding site 8 out of 32 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 8 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs108

b:77.8
occ:0.50
O2 A:C48 3.3 31.4 1.0
O2' A:C48 3.3 46.2 1.0
H1' A:G49 3.4 50.0 1.0
H1' A:C48 3.5 35.3 1.0
H4' A:G49 3.6 50.8 1.0
HO2' A:G49 3.7 59.1 1.0
O2' A:G49 3.8 49.3 1.0
H22 A:G23 3.8 41.8 1.0
O4' A:G49 3.8 48.6 1.0
H21 A:G23 3.8 41.8 1.0
H2' A:C48 3.9 38.8 1.0
C1' A:G49 4.0 41.6 1.0
C2' A:C48 4.0 32.3 1.0
N2 A:G23 4.1 34.8 1.0
C4' A:G49 4.2 42.4 1.0
C1' A:C48 4.2 29.4 1.0
C2 A:C48 4.4 35.6 1.0
C2' A:G49 4.5 46.8 1.0
N1 A:C48 4.8 40.8 1.0
O5' A:G49 5.0 38.2 1.0

Caesium binding site 9 out of 32 in 5d5l

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Caesium binding site 9 out of 32 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 9 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs109

b:0.2
occ:0.75
O2 A:C69 3.3 32.7 1.0
O2' A:C69 3.6 39.9 1.0
HO2' A:C69 3.8 47.9 1.0
H1' A:C69 3.9 32.0 1.0
H2' A:C69 4.3 34.5 1.0
C2' A:C69 4.3 28.8 1.0
H61 A:A55 4.4 43.4 1.0
C2 A:C69 4.5 32.8 1.0
C1' A:C69 4.5 26.7 1.0
H42 A:C56 4.6 46.8 1.0
HO2' A:A71 4.7 42.2 1.0
N3 A:C56 4.9 32.1 1.0
H5' A:A70 4.9 31.2 1.0

Caesium binding site 10 out of 32 in 5d5l

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Caesium binding site 10 out of 32 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 10 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs110

b:94.0
occ:0.50
H5 A:U35 2.5 0.6 1.0
H3' A:U34 3.2 0.7 1.0
C5 A:U35 3.3 99.7 1.0
O4 A:U35 3.4 87.9 1.0
O3' A:U34 3.5 98.5 1.0
O4 A:U36 3.7 64.0 1.0
C4 A:U35 3.7 92.3 1.0
C3' A:U34 3.9 0.7 1.0
C4 A:U36 3.9 64.2 1.0
H5 A:U36 4.0 79.5 1.0
C5 A:U36 4.1 66.3 1.0
OP2 A:U35 4.3 0.1 1.0
C6 A:U35 4.3 0.7 1.0
H6 A:U35 4.5 0.2 1.0
P A:U35 4.5 0.4 1.0
N3 A:U36 4.7 63.0 1.0
H61 A:A75 4.7 58.3 1.0
H5' A:U34 4.7 0.1 1.0
C6 A:U36 4.9 66.6 1.0
H3 A:U36 4.9 75.6 1.0
C2' A:U34 4.9 0.5 1.0
C4' A:U34 4.9 0.3 1.0
H4' A:U34 4.9 0.6 1.0
OP1 A:U35 5.0 0.2 1.0
O2' A:U34 5.0 0.2 1.0

Reference:

I.A.Belashov, J.A.Liberman, M.Salim, J.E.Wedekind. Cesium(I) Binding to G-U-Wobble Base Pairs in PREQ1 Riboswitches with Implications For Crystallographic Phasing To Be Published.
Page generated: Sun Dec 13 10:56:43 2020

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