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Caesium in PDB 5ddr: L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+

Protein crystallography data

The structure of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+, PDB code: 5ddr was solved by A.Ren, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.37 / 2.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.967, 86.882, 62.218, 90.00, 102.61, 90.00
R / Rfree (%) 21.2 / 27.1

Other elements in 5ddr:

The structure of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ also contains other interesting chemical elements:

Magnesium (Mg) 11 atoms
Potassium (K) 7 atoms
Sodium (Na) 4 atoms

Caesium Binding Sites:

The binding sites of Caesium atom in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ (pdb code 5ddr). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 7 binding sites of Caesium where determined in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+, PDB code: 5ddr:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Caesium binding site 1 out of 7 in 5ddr

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Caesium binding site 1 out of 7 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs112

b:64.6
occ:1.00
 O A:HOH298 2.5 39.9 1.0
O A:HOH213 2.6 34.6 1.0
O A:HOH238 2.6 32.6 1.0
O A:HOH276 2.6 28.0 1.0
O A:HOH268 2.6 35.9 1.0
N7 A:G11 3.7 28.3 1.0
O6 A:G12 3.7 30.3 1.0
N7 A:A10 4.1 31.9 1.0
O6 A:G11 4.1 29.7 1.0
N7 A:G12 4.2 30.8 1.0
O A:HOH211 4.3 39.9 1.0
C6 A:G12 4.4 31.1 1.0
MG A:MG108 4.5 41.5 1.0
N6 A:A10 4.5 28.6 1.0
O A:HOH258 4.5 34.3 1.0
C5 A:G11 4.6 28.4 1.0
C8 A:G11 4.6 29.2 1.0
C5 A:G12 4.6 31.4 1.0
C5 A:A10 4.7 30.9 1.0
C6 A:G11 4.7 29.5 1.0
C8 A:A10 4.8 31.9 1.0
C6 A:A10 4.9 29.9 1.0

Caesium binding site 2 out of 7 in 5ddr

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Caesium binding site 2 out of 7 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs113

b:65.1
occ:1.00
 O A:HOH206 2.5 39.9 1.0
O A:HOH272 2.6 39.7 1.0
O A:HOH223 2.6 38.8 1.0
N7 A:G20 2.8 38.4 1.0
K A:K103 3.4 42.0 1.0
O2' A:C21 3.6 36.1 1.0
C8 A:G20 3.8 35.5 1.0
C5 A:G20 3.9 35.6 1.0
O A:HOH265 3.9 37.2 1.0
N7 A:G19 3.9 30.8 1.0
O6 A:G20 4.0 38.2 1.0
O2 A:C21 4.0 39.7 1.0
O A:HOH219 4.0 32.6 1.0
O A:HOH310 4.2 31.4 1.0
MG A:MG106 4.3 40.2 1.0
C6 A:G20 4.3 35.2 1.0
O A:HOH304 4.5 43.8 1.0
C8 A:G19 4.6 33.4 1.0
C5 A:G19 4.6 33.1 1.0
C2 A:C21 4.6 37.8 1.0
O6 A:G19 4.7 34.8 1.0
C2' A:C21 4.8 36.7 1.0
OP2 A:G20 4.9 32.5 1.0
C6 A:G19 4.9 34.7 1.0

Caesium binding site 3 out of 7 in 5ddr

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Caesium binding site 3 out of 7 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs114

b:91.9
occ:1.00
 O A:HOH259 2.5 46.3 1.0
O A:HOH284 2.6 45.4 1.0
O A:HOH255 2.6 42.8 1.0
O6 A:G46 2.6 40.5 1.0
C6 A:G46 3.4 40.1 1.0
O A:HOH293 3.8 40.1 1.0
O6 A:G47 3.8 36.3 1.0
O4 A:U32 3.9 33.0 1.0
O A:HOH309 4.1 44.9 1.0
C5 A:G46 4.1 41.7 1.0
O A:HOH292 4.2 38.8 1.0
O A:HOH266 4.2 33.6 1.0
N7 A:G47 4.2 37.2 1.0
N7 A:G46 4.2 44.6 1.0
N4 A:C33 4.3 35.0 1.0
N1 A:G46 4.3 39.0 1.0
N4 A:C48 4.4 33.0 1.0
O6 A:G31 4.6 32.2 1.0
C6 A:G47 4.6 36.0 1.0
O A:HOH303 4.7 45.8 1.0
C5 A:G47 4.8 37.3 1.0
C4 A:U32 4.9 33.0 1.0
O A:HOH240 4.9 37.0 1.0
K A:K105 5.0 46.8 1.0

Caesium binding site 4 out of 7 in 5ddr

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Caesium binding site 4 out of 7 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs113

b:99.3
occ:1.00
 O B:HOH209 2.5 36.9 1.0
O B:HOH250 2.6 23.5 1.0
O2' B:C21 3.7 31.3 1.0
O2 B:C21 4.0 34.6 1.0
O B:HOH306 4.0 51.2 1.0
O B:HOH233 4.1 38.4 1.0
O B:HOH240 4.1 43.1 1.0
O B:HOH289 4.2 30.0 1.0
O3' B:C21 4.2 30.7 1.0
OP2 B:G22 4.4 35.3 1.0
C1' B:C21 4.6 32.2 1.0
C2' B:C21 4.6 34.4 1.0
C2 B:C21 4.8 34.1 1.0

Caesium binding site 5 out of 7 in 5ddr

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Caesium binding site 5 out of 7 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs114

b:90.5
occ:1.00
 O B:HOH232 2.6 32.4 1.0
O B:HOH266 2.7 25.6 1.0
N3 B:G22 3.8 27.9 1.0
N2 B:G22 3.9 26.7 1.0
N7 B:G54 3.9 27.9 1.0
O B:HOH289 4.0 30.0 1.0
C2 B:G22 4.0 27.7 1.0
O B:HOH241 4.1 26.5 1.0
C5' B:G22 4.2 28.2 1.0
OP2 B:G22 4.2 35.3 1.0
OP2 B:G2 4.3 25.7 1.0
OP2 B:G23 4.5 29.3 1.0
C8 B:G54 4.5 29.8 1.0
C4 B:G22 4.5 27.3 1.0
O4' B:G22 4.6 27.1 1.0
O5' B:G22 4.6 31.6 1.0
O B:HOH209 4.6 36.9 1.0
C4' B:G22 4.8 27.6 1.0
N1 B:G22 4.8 25.3 1.0
C3' B:G22 4.9 26.8 1.0
C5 B:G54 5.0 28.0 1.0

Caesium binding site 6 out of 7 in 5ddr

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Caesium binding site 6 out of 7 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs115

b:59.6
occ:1.00
 N7 B:G11 2.7 34.6 1.0
C8 B:G11 3.7 31.3 1.0
O6 B:G12 3.7 34.0 1.0
C5 B:G11 3.7 32.0 1.0
O6 B:G11 3.9 31.4 1.0
N7 B:G12 3.9 33.9 1.0
O B:HOH254 4.0 33.9 1.0
O B:HOH281 4.0 41.8 1.0
N7 B:A10 4.0 32.5 1.0
O B:HOH236 4.1 33.0 1.0
C6 B:G11 4.2 31.6 1.0
C6 B:G12 4.3 34.3 1.0
C5 B:G12 4.4 33.1 1.0
O B:HOH228 4.6 37.4 1.0
N6 B:A10 4.6 29.4 1.0
C5 B:A10 4.6 30.3 1.0
C8 B:A10 4.7 33.6 1.0
MG B:MG107 4.8 45.0 1.0
N9 B:G11 4.9 29.6 1.0
C6 B:A10 4.9 31.1 1.0
C4 B:G11 4.9 30.1 1.0
C8 B:G12 5.0 32.0 1.0

Caesium binding site 7 out of 7 in 5ddr

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Caesium binding site 7 out of 7 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs116

b:80.7
occ:1.00
 O3' B:G12 3.7 38.9 1.0
N7 B:A13 3.8 35.9 1.0
O2' B:G12 3.9 35.1 1.0
O B:HOH201 4.0 44.5 1.0
OP1 B:A13 4.1 36.2 1.0
C8 B:A13 4.4 36.7 1.0
N6 B:A14 4.5 33.6 1.0
P B:A13 4.5 40.3 1.0
C3' B:G12 4.6 37.2 1.0
C2' B:G12 4.8 34.6 1.0
C4' B:G12 4.9 33.7 1.0
N7 B:A14 4.9 35.4 1.0

Reference:

A.Ren, Y.Xue, A.Peselis, A.Serganov, H.M.Al-Hashimi, D.J.Patel. Structural and Dynamic Basis For Low-Affinity, High-Selectivity Binding of L-Glutamine By the Glutamine Riboswitch. Cell Rep V. 13 1800 2015.
ISSN: ESSN 2211-1247
PubMed: 26655897
DOI: 10.1016/J.CELREP.2015.10.062
Page generated: Sun Dec 13 10:56:42 2020

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