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Potassium 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
Caesium (Cs) 7 atoms
Sodium (Na) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 7 binding sites of Potassium where determined in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+, PDB code: 5ddr:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 5ddr

Go back to Potassium Binding Sites List in 5ddr
Potassium 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 Potassium with other atoms in the K 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:K102

b:50.2
occ:1.00
 O A:HOH282 2.4 44.1 1.0
O A:HOH208 3.1 36.2 1.0
O A:HOH246 3.2 35.7 1.0
O A:HOH297 3.2 39.0 1.0
MG A:MG109 3.6 41.0 1.0
O A:HOH277 3.8 46.0 1.0
N3 A:G22 3.9 38.0 1.0
N7 A:G54 3.9 37.6 1.0
K A:K103 3.9 42.0 1.0
C5' A:G22 4.0 35.6 1.0
N2 A:G22 4.0 35.0 1.0
O A:HOH281 4.1 37.3 1.0
C2 A:G22 4.1 36.7 1.0
OP2 A:G22 4.2 36.5 1.0
O5' A:G22 4.4 33.2 1.0
OP2 A:G23 4.4 38.2 1.0
C8 A:G54 4.5 37.3 1.0
O4' A:G22 4.5 34.0 1.0
OP2 A:G2 4.6 35.5 1.0
C4' A:G22 4.7 35.8 1.0
O A:HOH251 4.7 42.1 1.0
C4 A:G22 4.7 35.3 1.0
C3' A:G22 4.8 34.1 1.0
P A:G22 4.9 33.8 1.0
O A:HOH304 5.0 43.8 1.0

Potassium binding site 2 out of 7 in 5ddr

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Potassium 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 Potassium with other atoms in the K 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:K103

b:42.0
occ:1.00
 O A:HOH206 2.2 39.9 1.0
O A:HOH282 2.7 44.1 1.0
O A:HOH208 2.9 36.2 1.0
O A:HOH272 3.2 39.7 1.0
CS A:CS113 3.4 65.1 1.0
O A:HOH304 3.4 43.8 1.0
O A:HOH277 3.5 46.0 1.0
O A:HOH263 3.8 33.1 1.0
OP2 A:G22 3.9 36.5 1.0
K A:K102 3.9 50.2 1.0
O3' A:C21 4.0 34.1 1.0
MG A:MG109 4.1 41.0 1.0
O2' A:C21 4.1 36.1 1.0
O A:HOH297 4.4 39.0 1.0
O A:HOH281 4.5 37.3 1.0
O2 A:C21 4.6 39.7 1.0
P A:G22 4.6 33.8 1.0
O A:HOH273 4.8 33.9 1.0
C1' A:C21 4.9 33.8 1.0
C2' A:C21 4.9 36.7 1.0

Potassium binding site 3 out of 7 in 5ddr

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Potassium 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 Potassium with other atoms in the K 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:K104

b:62.0
occ:1.00
 O B:HOH206 2.5 24.1 1.0
O B:HOH290 2.8 32.2 1.0
OP2 B:C33 4.0 26.3 1.0
OP1 B:C33 4.0 28.1 1.0
O B:HOH217 4.2 32.8 1.0
C4' A:U17 4.4 33.1 1.0
O4' A:U17 4.4 32.5 1.0
O2' A:C16 4.5 32.7 1.0
P B:C33 4.6 27.4 1.0
C5' A:U17 4.7 32.4 1.0

Potassium binding site 4 out of 7 in 5ddr

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Potassium 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 Potassium with other atoms in the K 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
A:K105

b:46.8
occ:1.00
 N7 A:G31 2.6 32.6 1.0
O A:HOH259 2.6 46.3 1.0
O A:HOH293 2.6 40.1 1.0
O A:HOH240 2.8 37.0 1.0
O A:HOH249 2.8 38.2 1.0
C8 A:G31 3.4 30.8 1.0
O4 A:U32 3.5 33.0 1.0
C5 A:G31 3.7 31.3 1.0
N7 A:G30 3.7 31.9 1.0
O A:HOH234 3.8 34.3 1.0
O6 A:G31 3.9 32.2 1.0
C5 A:G30 3.9 31.1 1.0
O A:HOH292 3.9 38.8 1.0
C8 A:G30 4.0 33.3 1.0
C6 A:G31 4.1 30.0 1.0
C4 A:U32 4.2 33.0 1.0
OP2 A:G31 4.3 31.5 1.0
C6 A:G30 4.3 32.4 1.0
C5 A:U32 4.4 32.3 1.0
C4 A:G30 4.5 30.5 1.0
O A:HOH203 4.5 43.9 1.0
N9 A:G30 4.5 30.1 1.0
O6 A:G30 4.6 34.2 1.0
N9 A:G31 4.7 29.8 1.0
C4 A:G31 4.8 32.2 1.0
OP2 A:G30 4.9 38.8 1.0
CS A:CS114 5.0 91.9 1.0

Potassium binding site 5 out of 7 in 5ddr

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Potassium 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 Potassium with other atoms in the K 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:K102

b:39.1
occ:1.00
 O A:HOH202 2.0 24.3 1.0
O2' B:C33 3.4 25.1 1.0
N7 A:A13 3.7 27.6 1.0
O A:HOH306 3.7 28.3 1.0
O3' A:G12 3.8 28.8 1.0
O A:HOH235 3.8 37.4 1.0
O5' B:C34 4.0 26.4 1.0
OP1 A:A13 4.1 26.2 1.0
O2' A:G12 4.1 26.5 1.0
O B:HOH229 4.2 32.9 1.0
C8 A:A13 4.2 29.4 1.0
O3' B:C33 4.3 27.9 1.0
C2' B:C33 4.6 28.2 1.0
P A:A13 4.6 28.4 1.0
N6 A:A14 4.8 26.1 1.0
P B:C34 4.8 27.8 1.0
C3' A:G12 4.8 27.8 1.0
C5 A:A13 4.9 26.5 1.0
OP1 B:C34 4.9 30.4 1.0
N6 A:A13 5.0 25.2 1.0
C3' B:C33 5.0 26.8 1.0

Potassium binding site 6 out of 7 in 5ddr

Go back to Potassium Binding Sites List in 5ddr
Potassium 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 Potassium with other atoms in the K 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:K103

b:26.1
occ:1.00
 O B:HOH303 2.4 27.2 1.0
O B:HOH257 2.5 35.7 1.0
O B:HOH279 2.5 29.4 1.0
O B:HOH310 2.8 30.6 1.0
K B:K104 3.3 30.1 1.0
O6 B:G46 3.6 31.4 1.0
O4 B:U32 3.6 25.4 1.0
O B:HOH204 3.7 33.5 1.0
O6 B:G47 3.8 29.0 1.0
O B:HOH219 3.8 25.6 1.0
O6 B:G31 3.8 24.5 1.0
O B:HOH277 3.9 34.0 1.0
O B:HOH297 4.0 34.0 1.0
N4 B:C48 4.1 24.6 1.0
C6 B:G46 4.3 31.9 1.0
N4 B:C33 4.4 24.3 1.0
N7 B:G47 4.5 28.8 1.0
C4 B:U32 4.5 25.7 1.0
N3 B:U32 4.6 24.7 1.0
C6 B:G47 4.7 29.0 1.0
C6 B:G31 4.8 23.9 1.0
C5 B:G47 5.0 29.6 1.0

Potassium binding site 7 out of 7 in 5ddr

Go back to Potassium Binding Sites List in 5ddr
Potassium 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 Potassium with other atoms in the K 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:K104

b:30.1
occ:1.00
 O B:HOH303 2.1 27.2 1.0
O B:HOH285 2.5 25.6 1.0
N7 B:G31 2.7 23.3 1.0
K B:K103 3.3 26.1 1.0
O4 B:U32 3.4 25.4 1.0
O6 B:G31 3.5 24.5 1.0
O B:HOH310 3.6 30.6 1.0
N7 B:G30 3.6 25.0 1.0
O B:HOH219 3.6 25.6 1.0
C5 B:G31 3.6 23.6 1.0
C5 B:G30 3.8 22.0 1.0
O B:HOH224 3.8 24.7 1.0
C8 B:G31 3.9 23.1 1.0
O6 B:G30 3.9 22.2 1.0
C6 B:G30 3.9 23.2 1.0
C6 B:G31 3.9 23.9 1.0
O B:HOH280 4.0 30.6 1.0
O B:HOH279 4.1 29.4 1.0
O B:HOH246 4.1 30.7 1.0
C4 B:U32 4.2 25.7 1.0
C8 B:G30 4.3 25.1 1.0
O B:HOH268 4.3 25.3 1.0
O B:HOH302 4.3 31.6 1.0
C4 B:G30 4.5 23.2 1.0
N1 B:G30 4.8 24.5 1.0
N9 B:G30 4.8 23.9 1.0
C4 B:G31 4.9 23.0 1.0
C5 B:U32 4.9 24.7 1.0
N3 B:U32 4.9 24.7 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: Sat Aug 9 08:45:29 2025

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