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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: Tue Aug 20 15:34:46 2024

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