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Sodium in PDB 5ddp: L-Glutamine Riboswitch Bound with L-Glutamine

Protein crystallography data

The structure of L-Glutamine Riboswitch Bound with L-Glutamine, PDB code: 5ddp 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) 38.99 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.648, 86.205, 60.713, 90.00, 100.04, 90.00
R / Rfree (%) 19 / 24.3

Other elements in 5ddp:

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

Magnesium (Mg) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the L-Glutamine Riboswitch Bound with L-Glutamine (pdb code 5ddp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the L-Glutamine Riboswitch Bound with L-Glutamine, PDB code: 5ddp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 5ddp

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Sodium binding site 1 out of 10 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na107

b:32.2
occ:1.00
 N7 A:G11 2.2 33.2 1.0
O A:HOH219 2.4 38.5 1.0
O A:HOH261 2.5 36.5 1.0
O A:HOH320 2.5 39.8 1.0
O A:HOH332 2.5 43.6 1.0
C5 A:G11 3.2 30.0 1.0
C8 A:G11 3.3 32.3 1.0
O6 A:G12 3.3 36.6 1.0
O6 A:G11 3.4 33.1 1.0
N7 A:G12 3.6 31.3 1.0
C6 A:G11 3.7 31.6 1.0
C6 A:G12 3.9 34.7 1.0
C5 A:G12 4.0 33.6 1.0
N7 A:A10 4.0 36.7 1.0
MG A:MG105 4.1 56.2 1.0
O A:HOH350 4.2 49.4 1.0
C5 A:A10 4.4 30.5 1.0
C4 A:G11 4.4 30.2 1.0
O A:HOH330 4.4 40.0 1.0
N9 A:G11 4.4 29.7 1.0
N6 A:A10 4.5 32.3 1.0
C8 A:A10 4.6 36.6 1.0
C6 A:A10 4.6 31.4 1.0
O A:HOH263 4.6 38.1 1.0
C8 A:G12 4.7 31.9 1.0
O A:HOH305 4.7 45.3 1.0
O A:HOH255 4.9 39.9 1.0
O A:HOH347 5.0 49.6 1.0

Sodium binding site 2 out of 10 in 5ddp

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Sodium binding site 2 out of 10 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na108

b:33.8
occ:1.00
 O A:HOH345 2.3 47.7 1.0
N7 A:G20 2.3 37.6 1.0
O A:HOH314 2.6 39.5 1.0
O A:HOH294 2.7 42.3 1.0
O2' A:C21 2.7 35.2 1.0
C8 A:G20 3.3 37.2 1.0
C5 A:G20 3.4 37.9 1.0
O A:HOH309 3.4 34.4 1.0
O A:HOH207 3.4 44.0 1.0
O A:HOH262 3.5 35.5 1.0
O6 A:G20 3.6 40.1 1.0
O A:HOH353 3.6 46.7 1.0
C6 A:G20 3.9 37.9 1.0
N7 A:G19 3.9 36.5 1.0
O2 A:C21 3.9 31.7 1.0
C2' A:C21 4.0 35.8 1.0
O A:HOH340 4.1 51.5 1.0
C5 A:G19 4.2 37.1 1.0
C2 A:C21 4.2 36.3 1.0
O A:HOH316 4.4 45.1 1.0
O6 A:G19 4.4 37.1 1.0
C1' A:C21 4.5 35.0 1.0
C6 A:G19 4.5 38.8 1.0
C8 A:G19 4.5 36.7 1.0
N1 A:C21 4.5 33.9 1.0
N9 A:G20 4.5 38.0 1.0
C4 A:G20 4.6 38.3 1.0
OP2 A:G20 4.6 41.2 1.0
N3 A:C21 4.9 33.1 1.0

Sodium binding site 3 out of 10 in 5ddp

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Sodium binding site 3 out of 10 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na109

b:21.7
occ:1.00
 O A:HOH201 2.3 40.3 1.0
O6 A:G47 2.5 26.9 1.0
O A:HOH267 2.6 36.2 1.0
O A:HOH264 2.6 34.4 1.0
O4 A:U32 2.7 25.8 1.0
O6 A:G46 3.1 30.7 1.0
O A:HOH291 3.3 39.4 1.0
O6 A:G31 3.3 29.7 1.0
O A:HOH337 3.4 39.8 1.0
O A:HOH352 3.5 43.6 1.0
C6 A:G47 3.6 29.0 1.0
C4 A:U32 3.6 25.9 1.0
N4 A:C48 3.7 32.5 1.0
N4 A:C33 3.8 27.6 1.0
N3 A:U32 3.8 26.9 1.0
C6 A:G46 4.0 33.7 1.0
N7 A:G47 4.1 31.6 1.0
C5 A:G47 4.2 32.5 1.0
C6 A:G31 4.3 29.5 1.0
O A:HOH293 4.3 40.6 1.0
O A:HOH298 4.5 34.2 1.0
C4 A:C33 4.6 26.5 1.0
NA A:NA111 4.6 43.8 1.0
N1 A:G46 4.7 32.0 1.0
C4 A:C48 4.7 30.2 1.0
C5 A:G46 4.7 35.4 1.0
N1 A:G47 4.8 28.4 1.0
O A:HOH301 4.8 39.6 1.0
N3 A:C33 4.9 28.6 1.0

Sodium binding site 4 out of 10 in 5ddp

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Sodium binding site 4 out of 10 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na110

b:38.6
occ:1.00
 O A:HOH275 2.6 36.5 1.0
O2' A:G12 2.8 33.6 1.0
O2' B:C33 3.2 39.1 1.0
N7 A:A13 3.2 38.5 1.0
O3' A:G12 3.3 34.2 1.0
O3' B:C33 3.5 38.4 1.0
N6 A:A14 3.6 37.1 1.0
C8 A:A13 3.9 38.2 1.0
C2' A:G12 4.0 34.4 1.0
C3' A:G12 4.0 35.2 1.0
C5' B:C34 4.1 43.0 1.0
OP1 B:C34 4.2 40.6 1.0
C4' A:G12 4.3 34.3 1.0
OP1 A:A13 4.3 36.7 1.0
C2' B:C33 4.3 35.5 1.0
C3' B:C33 4.3 37.1 1.0
C5 A:A13 4.3 41.1 1.0
N7 A:A14 4.4 37.5 1.0
C6 A:A14 4.4 39.3 1.0
P A:A13 4.5 39.5 1.0
P B:C34 4.5 36.3 1.0
C4' B:C33 4.5 34.7 1.0
N6 A:A13 4.6 36.4 1.0
C5 A:A14 4.7 38.4 1.0
O5' B:C34 4.8 40.3 1.0
C6 A:A13 4.9 41.3 1.0
O5' A:A13 4.9 35.3 1.0

Sodium binding site 5 out of 10 in 5ddp

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Sodium binding site 5 out of 10 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na111

b:43.8
occ:1.00
 N7 A:G31 2.2 28.7 1.0
O A:HOH324 2.5 46.3 1.0
O A:HOH301 2.5 39.6 1.0
O A:HOH264 2.6 34.4 1.0
C8 A:G31 3.0 27.2 1.0
O4 A:U32 3.2 25.8 1.0
C5 A:G31 3.3 25.1 1.0
O A:HOH291 3.4 39.4 1.0
O A:HOH279 3.6 30.2 1.0
O6 A:G31 3.7 29.7 1.0
N7 A:G30 3.7 36.4 1.0
C4 A:U32 3.8 25.9 1.0
C5 A:G30 3.8 29.7 1.0
C6 A:G31 3.9 29.5 1.0
C5 A:U32 3.9 25.7 1.0
OP2 A:G31 4.0 36.1 1.0
C8 A:G30 4.1 33.6 1.0
C4 A:G30 4.2 31.9 1.0
C6 A:G30 4.2 30.1 1.0
N9 A:G31 4.2 27.8 1.0
N9 A:G30 4.4 32.5 1.0
C4 A:G31 4.4 25.2 1.0
O6 A:G30 4.6 33.6 1.0
O A:HOH313 4.6 39.8 1.0
NA A:NA109 4.6 21.7 1.0
O A:HOH337 4.7 39.8 1.0
O5' A:G31 4.8 31.3 1.0
N1 A:G30 4.8 29.9 1.0
C3' A:G30 4.9 33.2 1.0
C2' A:G30 4.9 33.8 1.0
N3 A:G30 4.9 30.7 1.0
N3 A:U32 5.0 26.9 1.0
O A:HOH210 5.0 40.4 1.0

Sodium binding site 6 out of 10 in 5ddp

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Sodium binding site 6 out of 10 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na106

b:35.9
occ:1.00
 N7 B:G11 2.2 28.5 1.0
O B:HOH246 2.3 44.2 1.0
O B:HOH295 2.4 47.6 1.0
O B:HOH208 2.4 33.2 1.0
O B:HOH265 2.6 39.9 1.0
O B:HOH245 2.7 45.0 1.0
C5 B:G11 3.2 30.5 1.0
C8 B:G11 3.2 28.3 1.0
O6 B:G11 3.4 29.2 1.0
N7 B:G12 3.5 27.1 1.0
O6 B:G12 3.6 31.0 1.0
C6 B:G11 3.7 27.9 1.0
O B:HOH298 3.7 49.2 1.0
N7 B:A10 3.9 34.0 1.0
C5 B:G12 4.1 26.7 1.0
MG B:MG105 4.1 56.0 1.0
C6 B:G12 4.1 30.5 1.0
C5 B:A10 4.2 31.2 1.0
C4 B:G11 4.4 28.4 1.0
N9 B:G11 4.4 27.0 1.0
C8 B:A10 4.4 32.1 1.0
N6 B:A10 4.5 31.6 1.0
C8 B:G12 4.5 29.0 1.0
C6 B:A10 4.6 30.4 1.0
O B:HOH217 4.6 36.6 1.0
O B:HOH236 4.7 40.2 1.0
C4 B:A10 5.0 27.5 1.0

Sodium binding site 7 out of 10 in 5ddp

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Sodium binding site 7 out of 10 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na107

b:34.5
occ:1.00
 O B:HOH254 2.5 35.4 1.0
O B:HOH252 2.6 45.8 1.0
O6 B:G46 2.8 38.5 1.0
O6 B:G47 2.8 32.5 1.0
O4 B:U32 2.8 30.5 1.0
O B:HOH215 3.3 36.3 1.0
O6 B:G31 3.4 27.5 1.0
N4 B:C33 3.6 37.0 1.0
O B:HOH303 3.7 50.0 1.0
C6 B:G46 3.7 39.3 1.0
C4 B:U32 3.8 30.7 1.0
N4 B:C48 3.8 32.0 1.0
O B:HOH202 3.9 44.6 1.0
C6 B:G47 3.9 32.8 1.0
N3 B:U32 3.9 28.6 1.0
N7 B:G47 4.2 37.4 1.0
O B:HOH239 4.3 39.0 1.0
O B:HOH262 4.3 46.6 1.0
NA B:NA110 4.4 40.1 1.0
C6 B:G31 4.4 27.7 1.0
C5 B:G47 4.4 36.7 1.0
C5 B:G46 4.4 41.1 1.0
N1 B:G46 4.5 38.0 1.0
C4 B:C33 4.6 36.5 1.0
N7 B:G46 4.6 45.7 1.0
C4 B:C48 4.8 32.4 1.0
N3 B:C33 4.9 36.0 1.0

Sodium binding site 8 out of 10 in 5ddp

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Sodium binding site 8 out of 10 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na108

b:38.7
occ:1.00
 N7 B:G20 2.2 40.5 1.0
O B:HOH209 2.3 46.2 1.0
O B:HOH293 2.4 49.1 1.0
O B:HOH228 2.6 42.4 1.0
C8 B:G20 3.2 35.9 1.0
O2' B:C21 3.2 39.1 1.0
C5 B:G20 3.2 38.1 1.0
O B:HOH241 3.4 39.1 1.0
O6 B:G20 3.5 39.5 1.0
O B:HOH219 3.5 42.9 1.0
N7 B:G19 3.5 35.9 1.0
O B:HOH211 3.6 46.8 1.0
C6 B:G20 3.7 40.8 1.0
C5 B:G19 3.8 35.5 1.0
O2 B:C21 3.9 39.2 1.0
C6 B:G19 4.1 38.6 1.0
O6 B:G19 4.1 37.2 1.0
C8 B:G19 4.1 35.1 1.0
C2 B:C21 4.2 42.1 1.0
O B:HOH280 4.2 38.8 1.0
C2' B:C21 4.4 42.5 1.0
N9 B:G20 4.4 38.1 1.0
C4 B:G20 4.4 38.1 1.0
N1 B:C21 4.6 42.1 1.0
C4 B:G19 4.6 35.6 1.0
OP2 B:G20 4.7 36.1 1.0
N3 B:C21 4.7 41.0 1.0
O B:HOH296 4.7 42.2 1.0
C1' B:C21 4.7 39.2 1.0
N9 B:G19 4.8 36.2 1.0
N1 B:G19 5.0 33.4 1.0

Sodium binding site 9 out of 10 in 5ddp

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Sodium binding site 9 out of 10 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na109

b:39.5
occ:1.00
 O B:HOH243 2.6 34.8 1.0
N7 B:A13 3.2 31.7 1.0
O2' B:G12 3.3 30.4 1.0
O3' B:G12 3.5 36.8 1.0
N6 B:A14 3.9 30.1 1.0
C8 B:A13 3.9 33.2 1.0
OP1 B:A13 4.3 39.5 1.0
C3' B:G12 4.3 30.6 1.0
C5 B:A13 4.3 31.9 1.0
N6 B:A13 4.3 32.3 1.0
C2' B:G12 4.4 31.5 1.0
C4' B:G12 4.5 32.5 1.0
P B:A13 4.6 32.9 1.0
C6 B:A14 4.6 30.9 1.0
N7 B:A14 4.6 31.2 1.0
C6 B:A13 4.8 34.2 1.0
C5 B:A14 4.9 28.9 1.0

Sodium binding site 10 out of 10 in 5ddp

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Sodium binding site 10 out of 10 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na110

b:40.1
occ:1.00
 N7 B:G31 2.3 31.9 1.0
O B:HOH239 2.4 39.0 1.0
O B:HOH244 2.5 38.0 1.0
O B:HOH254 2.5 35.4 1.0
O4 B:U32 3.2 30.5 1.0
C8 B:G31 3.3 30.8 1.0
C5 B:G31 3.4 29.6 1.0
O B:HOH303 3.7 50.0 1.0
O6 B:G31 3.7 27.5 1.0
N7 B:G30 3.8 27.1 1.0
C4 B:U32 3.9 30.7 1.0
C5 B:G30 3.9 27.7 1.0
C6 B:G31 3.9 27.7 1.0
O B:HOH258 4.0 34.0 1.0
C5 B:U32 4.1 29.7 1.0
C6 B:G30 4.2 30.9 1.0
C8 B:G30 4.3 28.9 1.0
O6 B:G30 4.3 31.1 1.0
NA B:NA107 4.4 34.5 1.0
C4 B:G30 4.5 27.9 1.0
N9 B:G31 4.5 27.6 1.0
OP2 B:G31 4.5 36.8 1.0
C4 B:G31 4.6 29.5 1.0
N9 B:G30 4.7 29.7 1.0
O B:HOH262 4.8 46.6 1.0
N1 B:G30 4.9 30.0 1.0
N3 B:U32 5.0 28.6 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: Mon Oct 7 20:33:07 2024

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