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Magnesium 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:

Sodium (Na) 10 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 9 in 5ddp

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Magnesium binding site 1 out of 9 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:34.3
occ:1.00
 OXT A:GLN101 1.9 25.2 1.0
O A:HOH281 2.1 30.6 1.0
O A:HOH237 2.1 27.5 1.0
O A:HOH240 2.1 30.0 1.0
O A:HOH285 2.1 31.3 1.0
O A:HOH241 2.1 25.6 1.0
C A:GLN101 2.9 29.7 1.0
O A:GLN101 3.2 27.0 1.0
N2 A:G54 3.7 30.1 1.0
OP2 A:A57 3.9 36.5 1.0
OP1 A:G54 4.0 26.6 1.0
N7 A:G22 4.1 28.8 1.0
O6 A:G22 4.2 30.1 1.0
CA A:GLN101 4.3 26.9 1.0
OP2 A:A56 4.3 32.0 1.0
N7 A:A57 4.4 32.0 1.0
C2 A:G54 4.5 29.6 1.0
O A:HOH280 4.5 43.6 1.0
CG A:GLN101 4.6 27.7 1.0
O A:HOH232 4.7 35.2 1.0
CB A:GLN101 4.8 29.9 1.0
N1 A:G54 4.8 29.9 1.0
C8 A:A57 4.8 32.9 1.0
C5 A:G22 4.9 27.8 1.0
C6 A:G22 5.0 27.5 1.0

Magnesium binding site 2 out of 9 in 5ddp

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Magnesium binding site 2 out of 9 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:34.5
occ:1.00
 O A:HOH218 2.0 34.0 1.0
O A:HOH245 2.1 30.0 1.0
O A:HOH351 2.1 24.1 1.0
O A:HOH269 2.1 27.4 1.0
O A:HOH348 2.1 33.3 1.0
O A:HOH248 2.2 28.8 1.0
O A:HOH335 4.0 38.4 1.0
O6 A:G54 4.0 34.1 1.0
O4 A:U3 4.1 27.6 1.0
O4 A:U4 4.1 31.4 1.0
O A:HOH235 4.3 36.3 1.0
O A:HOH309 4.3 34.4 1.0
O A:HOH282 4.3 32.1 1.0
O6 A:G5 4.3 36.5 1.0
O A:HOH287 4.4 34.9 1.0
N7 A:G54 4.4 28.8 1.0
O A:HOH355 4.5 45.3 1.0
C4 A:U3 4.7 29.9 1.0
N4 A:C55 4.8 34.0 1.0
C5 A:U3 4.9 32.0 1.0
C6 A:G54 4.9 31.2 1.0

Magnesium binding site 3 out of 9 in 5ddp

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Magnesium binding site 3 out of 9 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:65.0
occ:1.00
 O A:HOH236 2.1 39.5 1.0
O A:HOH220 2.1 39.2 1.0
O A:HOH340 3.1 51.5 1.0
O A:HOH262 3.4 35.5 1.0
O A:HOH207 3.6 44.0 1.0
O A:HOH206 4.1 43.8 1.0
O4 A:U17 4.3 32.2 1.0
N7 A:G18 4.4 34.9 1.0
O6 A:G18 4.4 34.3 1.0
C5 A:U17 4.4 33.9 1.0
C4 A:U17 4.6 34.5 1.0
O A:HOH345 4.6 47.7 1.0
O6 A:G19 4.9 37.1 1.0

Magnesium binding site 4 out of 9 in 5ddp

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Magnesium binding site 4 out of 9 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:56.2
occ:1.00
 O A:HOH255 2.1 39.9 1.0
O A:HOH347 2.1 49.6 1.0
O A:HOH261 2.1 36.5 1.0
O A:HOH332 2.9 43.6 1.0
O A:HOH349 3.1 45.4 1.0
O A:HOH277 3.1 35.9 1.0
O A:HOH350 3.3 49.4 1.0
N7 A:G12 4.0 31.3 1.0
NA A:NA107 4.1 32.2 1.0
O6 A:G12 4.1 36.6 1.0
O A:HOH263 4.4 38.1 1.0
O A:HOH254 4.5 38.0 1.0
C5 A:G12 4.6 33.6 1.0
C6 A:G12 4.6 34.7 1.0
OP1 A:A14 4.7 36.5 1.0
C8 A:G12 4.9 31.9 1.0

Magnesium binding site 5 out of 9 in 5ddp

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Magnesium binding site 5 out of 9 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:52.8
occ:1.00
 O A:HOH203 2.1 58.3 1.0
O3' A:G61 2.4 61.5 1.0
C3' A:G61 2.8 52.8 1.0
C2' A:G61 3.1 52.5 1.0
O2' A:G61 3.8 53.5 1.0
C4' A:G61 4.3 52.8 1.0
C1' A:G61 4.5 49.1 1.0
N9 A:G61 4.8 45.7 1.0

Magnesium binding site 6 out of 9 in 5ddp

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Magnesium binding site 6 out of 9 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:38.0
occ:1.00
 O B:HOH263 2.0 36.8 1.0
O B:GLN101 2.1 32.5 1.0
O B:HOH237 2.1 35.1 1.0
O B:HOH238 2.1 37.1 1.0
O B:HOH261 2.1 40.8 1.0
O B:HOH232 2.1 36.9 1.0
C B:GLN101 3.2 40.4 1.0
OXT B:GLN101 3.5 39.6 1.0
N2 B:G54 3.9 42.4 1.0
OP2 B:A57 4.0 48.5 1.0
OP1 B:G54 4.0 37.7 1.0
N7 B:G22 4.1 35.6 1.0
OP2 B:A56 4.1 45.4 1.0
O6 B:G22 4.4 44.0 1.0
N7 B:A57 4.4 49.0 1.0
C2 B:G54 4.5 40.3 1.0
CA B:GLN101 4.5 40.1 1.0
CG B:GLN101 4.8 36.6 1.0
O B:HOH276 4.8 43.6 1.0
N1 B:G54 4.8 39.7 1.0
CB B:GLN101 4.9 36.4 1.0
C5 B:G22 4.9 38.2 1.0
C8 B:A57 4.9 49.3 1.0

Magnesium binding site 7 out of 9 in 5ddp

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Magnesium binding site 7 out of 9 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:58.0
occ:1.00
 O B:HOH235 2.1 49.1 1.0
O B:HOH211 2.1 46.8 1.0
O B:HOH304 2.1 55.5 1.0
O B:HOH253 2.1 40.1 1.0
O B:HOH241 3.6 39.1 1.0
O B:HOH228 3.7 42.4 1.0
O6 B:G19 4.0 37.2 1.0
O6 B:G18 4.3 36.8 1.0
N7 B:G18 4.5 34.7 1.0
N4 B:C7 4.9 53.8 1.0
C6 B:G19 5.0 38.6 1.0
N4 B:C8 5.0 44.6 1.0

Magnesium binding site 8 out of 9 in 5ddp

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Magnesium binding site 8 out of 9 in the L-Glutamine Riboswitch Bound with L-Glutamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:49.2
occ:1.00
 O B:HOH301 2.1 36.8 1.0
O B:HOH275 2.1 38.5 1.0
O B:HOH216 2.1 44.2 1.0
O B:HOH296 2.1 42.2 1.0
O B:HOH279 2.1 38.8 1.0
O B:HOH249 2.1 43.3 1.0
O B:HOH280 3.5 38.8 1.0
O B:HOH277 4.1 37.2 1.0
O B:HOH250 4.1 47.5 1.0
O B:HOH219 4.2 42.9 1.0
O B:HOH242 4.2 36.8 1.0
O4 B:U4 4.2 50.4 1.0
O4 B:U3 4.5 45.3 1.0
O6 B:G5 4.6 52.4 1.0
O6 B:G54 4.7 39.0 1.0
O B:HOH209 4.8 46.2 1.0
N7 B:G54 4.9 38.5 1.0

Magnesium binding site 9 out of 9 in 5ddp

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of L-Glutamine Riboswitch Bound with L-Glutamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg105

b:56.0
occ:1.00
 O B:HOH208 2.1 33.2 1.0
O B:HOH297 2.1 42.6 1.0
O B:HOH289 2.1 36.3 1.0
O B:HOH298 2.2 49.2 1.0
O B:HOH217 3.1 36.6 1.0
O B:HOH255 3.3 35.7 1.0
O B:HOH236 3.7 40.2 1.0
O B:HOH295 4.0 47.6 1.0
N7 B:G12 4.0 27.1 1.0
NA B:NA106 4.1 35.9 1.0
O6 B:G12 4.7 31.0 1.0
O B:HOH212 4.7 33.2 1.0
O B:HOH265 4.8 39.9 1.0
C8 B:G12 4.9 29.0 1.0
C5 B:G12 4.9 26.7 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: Sun Sep 29 02:41:23 2024

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