Atomistry » Magnesium » PDB 5dar-5djg » 5ddp
Atomistry »
  Magnesium »
    PDB 5dar-5djg »
      5ddp »

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

Go back to Magnesium Binding Sites List in 5ddp
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

Go back to Magnesium Binding Sites List in 5ddp
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

Go back to Magnesium Binding Sites List in 5ddp
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

Go back to Magnesium Binding Sites List in 5ddp
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

Go back to Magnesium Binding Sites List in 5ddp
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

Go back to Magnesium Binding Sites List in 5ddp
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

Go back to Magnesium Binding Sites List in 5ddp
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

Go back to Magnesium Binding Sites List in 5ddp
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

Go back to Magnesium Binding Sites List in 5ddp
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy