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Magnesium in PDB 4tzx: Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+

Protein crystallography data

The structure of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+, PDB code: 4tzx was solved by J.Zhang, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.21 / 2.01
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 49.641, 152.839, 24.991, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+ (pdb code 4tzx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+, PDB code: 4tzx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4tzx

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Magnesium binding site 1 out of 9 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+


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 Variant, Grown in MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg102

b:44.6
occ:1.00
 O X:HOH257 2.1 43.8 1.0
O X:HOH283 2.1 31.9 1.0
O X:HOH285 2.1 40.3 1.0
O X:HOH261 2.2 28.9 1.0
O X:HOH244 2.3 25.6 1.0
O X:HOH294 3.9 37.5 1.0
OP2 X:A45 4.2 31.1 1.0
N7 X:G46 4.3 24.2 1.0
O4 X:U47 4.3 25.8 1.0
O X:HOH241 4.4 28.9 1.0
O6 X:G46 4.6 27.5 1.0

Magnesium binding site 2 out of 9 in 4tzx

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Magnesium binding site 2 out of 9 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+


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 Variant, Grown in MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg103

b:42.0
occ:1.00
 OP1 X:A24 2.0 30.7 1.0
O X:HOH302 2.1 45.1 1.0
O X:HOH272 2.1 29.5 1.0
O X:HOH242 2.1 26.5 1.0
O X:HOH246 2.2 25.8 1.0
O X:HOH251 2.3 41.5 1.0
P X:A24 3.5 29.9 1.0
O X:HOH266 3.9 28.9 1.0
O X:HOH293 3.9 41.6 1.0
O X:HOH258 4.0 31.9 1.0
O X:HOH267 4.1 30.5 1.0
O5' X:A24 4.2 26.4 1.0
N7 X:A24 4.3 29.1 1.0
OP2 X:A24 4.3 29.6 1.0
C8 X:A24 4.3 28.1 1.0
O X:HOH273 4.4 43.6 1.0
N7 X:G72 4.4 29.1 1.0
O6 X:G72 4.4 26.4 1.0
O3' X:A23 4.4 31.6 1.0
O X:HOH262 4.6 43.2 1.0
O X:HOH260 4.7 24.8 1.0
O X:HOH268 4.7 32.3 1.0
C5 X:U71 5.0 31.2 1.0

Magnesium binding site 3 out of 9 in 4tzx

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Magnesium binding site 3 out of 9 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+


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 Variant, Grown in MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg104

b:52.9
occ:1.00
 O X:HOH211 2.6 46.5 1.0
OP1 X:G44 4.2 41.4 1.0
C5' X:G44 4.5 34.7 1.0

Magnesium binding site 4 out of 9 in 4tzx

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Magnesium binding site 4 out of 9 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+


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 Variant, Grown in MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg105

b:48.4
occ:1.00
 O X:HOH295 2.1 51.1 1.0
O X:HOH264 2.3 41.0 1.0
O X:HOH249 2.4 42.3 1.0
O X:HOH270 2.6 38.2 1.0
N7 X:G43 3.1 29.0 1.0
O X:HOH288 3.3 35.8 1.0
O6 X:G43 3.8 28.0 1.0
C5 X:G43 4.0 28.5 1.0
C8 X:G43 4.1 29.3 1.0
C6 X:G43 4.2 27.9 1.0
O X:HOH301 4.3 43.7 1.0
N7 X:G44 4.7 29.5 1.0
N7 X:G42 4.7 30.9 1.0
OP2 X:G43 4.8 31.8 1.0
O6 X:G44 4.9 27.8 1.0
OP2 X:G42 4.9 35.1 1.0

Magnesium binding site 5 out of 9 in 4tzx

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Magnesium binding site 5 out of 9 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+


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 Variant, Grown in MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg106

b:59.7
occ:1.00
 O X:HOH297 2.1 43.1 1.0
O X:HOH303 2.1 39.5 1.0
OP2 X:A23 2.5 41.7 1.0
O X:HOH248 3.4 29.8 1.0
O X:HOH311 3.4 62.6 1.0
P X:A23 3.9 40.2 1.0
O X:HOH259 4.2 31.5 1.0
O X:HOH273 4.3 43.6 1.0
OP1 X:A23 4.6 41.4 1.0
O3' X:U22 4.6 31.6 1.0
O5' X:A23 5.0 36.4 1.0

Magnesium binding site 6 out of 9 in 4tzx

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Magnesium binding site 6 out of 9 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+


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 Variant, Grown in MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg107

b:37.4
occ:1.00
 O X:HOH282 2.1 32.4 1.0
O X:HOH291 2.1 38.1 1.0
O2' X:G38 2.6 37.1 1.0
N2 X:G32 3.0 34.7 1.0
C6 X:A33 3.4 36.9 1.0
N1 X:A33 3.5 37.6 1.0
N6 X:A33 3.5 35.7 1.0
N1 X:G32 3.5 34.2 1.0
C2 X:G32 3.7 34.5 1.0
C2' X:G38 3.8 38.0 1.0
O X:HOH306 3.9 53.8 1.0
C5 X:A33 4.0 37.5 1.0
O X:HOH279 4.1 40.2 1.0
C4' X:G38 4.1 38.7 1.0
C2 X:A33 4.1 38.5 1.0
C1' X:G38 4.2 39.7 1.0
O4' X:G38 4.3 40.1 1.0
C3' X:G38 4.3 37.7 1.0
O3' X:G38 4.3 36.5 1.0
N7 X:A66 4.4 38.0 1.0
C4 X:A33 4.6 37.0 1.0
C5 X:U39 4.6 30.6 1.0
C6 X:G32 4.7 33.5 1.0
N3 X:A33 4.7 37.7 1.0
N7 X:A33 4.8 35.6 1.0
N6 X:A66 4.8 39.6 1.0
C5 X:A66 4.9 38.2 1.0
O6 X:G32 4.9 32.6 1.0

Magnesium binding site 7 out of 9 in 4tzx

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Magnesium binding site 7 out of 9 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg108

b:43.9
occ:1.00
 O X:HOH288 2.4 35.8 1.0
O6 X:G42 2.6 29.8 1.0
O4 X:U28 2.8 29.6 1.0
O X:HOH301 2.9 43.7 1.0
O6 X:G43 3.0 28.0 1.0
O4 X:U41 3.5 33.3 1.0
N4 X:C27 3.7 27.8 1.0
C4 X:U28 3.7 30.0 1.0
C6 X:G42 3.7 30.2 1.0
N3 X:U28 3.8 30.7 1.0
C6 X:G43 3.9 27.9 1.0
N6 X:A29 4.1 34.6 1.0
C4 X:U41 4.2 33.2 1.0
N7 X:G42 4.3 30.9 1.0
O X:HOH271 4.3 38.4 1.0
O X:HOH247 4.4 30.4 1.0
C5 X:G42 4.4 30.8 1.0
O X:HOH295 4.5 51.1 1.0
C5 X:G43 4.7 28.5 1.0
N1 X:G43 4.7 27.5 1.0
N3 X:U41 4.7 33.3 1.0
C4 X:C27 4.7 28.0 1.0
C6 X:A29 4.7 35.1 1.0
N7 X:G43 4.9 29.0 1.0
N1 X:G42 4.9 30.4 1.0

Magnesium binding site 8 out of 9 in 4tzx

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Magnesium binding site 8 out of 9 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg109

b:63.6
occ:1.00
 O X:HOH219 2.1 59.3 1.0
O X:HOH207 2.1 32.3 1.0
OP1 X:U40 3.5 48.1 1.0
OP1 X:A55 4.1 33.3 1.0
OP2 X:U41 4.6 35.1 1.0
P X:U40 4.7 46.6 1.0

Magnesium binding site 9 out of 9 in 4tzx

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Magnesium binding site 9 out of 9 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg110

b:52.1
occ:1.00
 O X:HOH308 2.9 51.2 1.0
O4 X:U77 3.0 46.6 1.0
N7 X:A76 3.5 32.9 1.0
O X:HOH309 3.7 49.9 1.0
C4 X:U77 4.0 46.6 1.0
N6 X:A76 4.0 33.4 1.0
C5 X:U77 4.3 46.3 1.0
C5 X:A76 4.3 32.9 1.0
C5 X:U75 4.4 29.6 1.0
C8 X:A76 4.5 31.9 1.0
C6 X:A76 4.5 33.1 1.0
O4 X:U75 4.6 29.3 1.0
C4 X:U75 4.6 29.1 1.0
N6 X:A19 5.0 53.3 1.0

Reference:

J.Zhang, A.R.Ferre-D'amare. Dramatic Improvement of Crystals of Large Rnas By Cation Replacement and Dehydration. Structure V. 22 1363 2014.
ISSN: ISSN 0969-2126
PubMed: 25185828
DOI: 10.1016/J.STR.2014.07.011
Page generated: Tue Aug 20 04:21:19 2024

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