Atomistry » Magnesium » PDB 4xgq-4xsz » 4xnr
Atomistry »
  Magnesium »
    PDB 4xgq-4xsz »
      4xnr »

Magnesium in PDB 4xnr: Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine

Protein crystallography data

The structure of Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine, PDB code: 4xnr was solved by J.Zhang, Y.Liu, Y.-X.Wang, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.13 / 2.21
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 49.482, 154.682, 25.178, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine (pdb code 4xnr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine, PDB code: 4xnr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4xnr

Go back to Magnesium Binding Sites List in 4xnr
Magnesium binding site 1 out of 6 in the Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg102

b:72.3
occ:1.00
 O X:HOH243 2.1 56.9 1.0
O X:HOH238 2.3 40.0 1.0
O X:HOH224 2.3 36.2 1.0
OP2 X:A45 3.8 54.3 1.0
O X:HOH221 4.4 40.3 1.0
N7 X:G46 4.5 44.7 1.0
O4 X:U47 4.6 46.2 1.0
O6 X:G46 4.6 41.1 1.0

Magnesium binding site 2 out of 6 in 4xnr

Go back to Magnesium Binding Sites List in 4xnr
Magnesium binding site 2 out of 6 in the Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg103

b:68.2
occ:1.00
 O X:HOH260 2.1 74.9 1.0
OP1 X:A24 2.1 47.0 1.0
O X:HOH226 2.1 49.9 1.0
O X:HOH225 2.1 45.6 1.0
O X:HOH227 2.2 44.5 1.0
O X:HOH228 2.2 46.3 1.0
P X:A24 3.6 46.1 1.0
O X:HOH252 4.0 36.9 1.0
O X:HOH253 4.1 44.4 1.0
O5' X:A24 4.3 44.4 1.0
N7 X:A24 4.3 45.4 1.0
N7 X:G72 4.4 51.8 1.0
O3' X:A23 4.4 46.9 1.0
C8 X:A24 4.4 43.6 1.0
O6 X:G72 4.5 49.3 1.0
OP2 X:A24 4.5 46.9 1.0
O X:HOH261 4.6 52.8 1.0
O X:HOH263 4.6 48.9 1.0

Magnesium binding site 3 out of 6 in 4xnr

Go back to Magnesium Binding Sites List in 4xnr
Magnesium binding site 3 out of 6 in the Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg104

b:55.2
occ:1.00
 O2 X:U47 2.6 44.4 1.0
N4 X:C50 2.8 46.2 1.0
C2 X:U49 3.1 55.9 1.0
N3 X:U49 3.1 55.4 1.0
N9 X:ADE101 3.2 45.0 1.0
N3 X:A21 3.3 47.1 1.0
O2 X:U49 3.4 56.2 1.0
C8 X:ADE101 3.5 43.8 1.0
N1 X:U49 3.5 56.6 1.0
C4 X:U49 3.7 55.6 1.0
C4 X:C50 3.7 48.4 1.0
C2 X:A21 3.7 47.4 1.0
C5 X:C50 3.8 49.6 1.0
C2 X:U47 3.8 45.5 1.0
O2' X:U49 3.8 55.1 1.0
O4 X:U51 3.9 44.6 1.0
C6 X:U49 4.0 56.5 1.0
C4 X:ADE101 4.0 43.7 1.0
C5 X:U49 4.1 56.0 1.0
C1' X:U49 4.3 58.2 1.0
O4 X:U49 4.3 56.0 1.0
O2' X:A21 4.4 47.2 1.0
N7 X:ADE101 4.4 42.1 1.0
N3 X:A76 4.4 53.4 1.0
N3 X:U47 4.4 44.9 1.0
C2' X:U49 4.5 57.4 1.0
C4 X:A21 4.5 47.4 1.0
C4 X:U51 4.6 45.3 1.0
O2 X:U75 4.6 44.7 1.0
C5 X:ADE101 4.7 41.9 1.0
N3 X:ADE101 4.7 44.0 1.0
C1' X:A21 4.7 48.4 1.0
N3 X:U51 4.8 44.7 1.0
N1 X:U47 4.9 47.6 1.0
C2 X:A76 4.9 54.0 1.0
N3 X:C50 4.9 50.4 1.0
C1' X:U47 4.9 49.1 1.0
C4 X:A76 4.9 54.0 1.0
C2' X:A21 5.0 47.4 1.0

Magnesium binding site 4 out of 6 in 4xnr

Go back to Magnesium Binding Sites List in 4xnr
Magnesium binding site 4 out of 6 in the Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg105

b:83.8
occ:1.00
 O X:HOH231 2.2 83.7 1.0
O X:HOH257 2.3 69.5 1.0
O X:HOH229 2.4 62.3 1.0
O X:HOH230 2.4 49.4 1.0
O X:HOH234 4.4 43.3 1.0
O6 X:G44 4.6 44.2 1.0
N7 X:G43 4.7 47.0 1.0
O X:HOH258 4.8 64.7 1.0
O6 X:G43 4.8 44.0 1.0
N7 X:G44 4.9 46.8 1.0

Magnesium binding site 5 out of 6 in 4xnr

Go back to Magnesium Binding Sites List in 4xnr
Magnesium binding site 5 out of 6 in the Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg106

b:82.4
occ:1.00
 O X:HOH244 2.1 52.5 1.0
O X:HOH237 2.2 44.1 1.0
O X:HOH255 2.4 87.3 1.0
O X:HOH223 2.6 42.8 1.0
OP2 X:A23 3.0 51.4 1.0
O X:HOH262 3.9 56.3 1.0
N6 X:A21 4.3 49.9 1.0
P X:A23 4.3 50.0 1.0
O3' X:U22 4.4 47.8 1.0
N6 X:ADE101 4.6 36.6 1.0
O4 X:U74 4.8 51.5 1.0
O2' X:U22 4.8 46.4 1.0
N7 X:A21 5.0 47.4 1.0

Magnesium binding site 6 out of 6 in 4xnr

Go back to Magnesium Binding Sites List in 4xnr
Magnesium binding site 6 out of 6 in the Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized By Position-Selective Labeling of Rna (Plor), in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg107

b:0.1
occ:1.00
 O X:HOH218 2.1 72.1 1.0
O X:HOH208 2.2 74.8 1.0
O X:HOH210 2.2 66.7 1.0
O X:HOH212 4.1 51.4 1.0
O6 X:G32 4.1 49.7 1.0
N7 X:G32 4.5 50.4 1.0
O X:HOH235 4.5 60.5 1.0
O4 X:U31 4.6 50.9 1.0
C5 X:U31 4.9 51.9 1.0
C6 X:G32 4.9 49.5 1.0
C4 X:U31 4.9 51.3 1.0

Reference:

Y.Liu, E.Holmstrom, J.Zhang, P.Yu, J.Wang, M.A.Dyba, J.Ying, S.Lockett, D.J.Nesbitt, A.R.Ferre-D'amare, R.Sousa, J.R.Stagno, Y.X.Wang. Synthesis and Applications of Rnas with Position-Selective Labelling and Mosaic Composition. Nature 2015.
ISSN: ESSN 1476-4687
PubMed: 25938715
DOI: 10.1038/NATURE14352
Page generated: Mon Dec 14 19:47:23 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy