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Magnesium in PDB 4en5: Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked

Protein crystallography data

The structure of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked, PDB code: 4en5 was solved by A.M.Ren, K.R.Rajashankar, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.36 / 2.96
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.205, 77.287, 42.597, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.1

Other elements in 4en5:

The structure of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked also contains other interesting chemical elements:

Fluorine (F) 1 atom
Thallium (Tl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked (pdb code 4en5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked, PDB code: 4en5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4en5

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Magnesium binding site 1 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:60.6
occ:1.00
 O A:HOH206 2.1 61.8 1.0
O A:HOH204 2.1 70.8 1.0
O A:HOH205 2.1 70.4 1.0
O6 A:G29 2.5 70.5 1.0
C6 A:G29 3.1 64.7 1.0
N7 A:G29 3.4 64.5 1.0
C5 A:G29 3.5 60.8 1.0
N1 A:G29 4.2 62.2 1.0
C8 A:G29 4.6 64.9 1.0
C4 A:G29 4.7 60.9 1.0
OP2 A:A31 4.8 62.0 1.0

Magnesium binding site 2 out of 9 in 4en5

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Magnesium binding site 2 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:60.4
occ:1.00
 F A:F110 1.8 67.4 1.0
OP2 A:G42 2.0 62.4 1.0
O A:HOH217 2.0 57.6 1.0
OP1 A:U41 2.0 61.9 1.0
OP2 A:A6 2.1 66.5 1.0
OP2 A:U7 2.1 59.2 1.0
MG A:MG103 2.7 61.7 1.0
P A:G42 2.9 61.8 1.0
O A:HOH215 3.0 60.5 1.0
O A:HOH214 3.0 65.9 1.0
OP1 A:G42 3.1 64.8 1.0
P A:A6 3.2 58.3 1.0
P A:U7 3.2 56.2 1.0
OP1 A:A6 3.4 65.5 1.0
P A:U41 3.4 56.5 1.0
MG A:MG104 3.5 72.4 1.0
OP1 A:U7 3.5 67.2 1.0
O A:HOH203 3.7 66.1 1.0
O3' A:U41 3.7 66.3 1.0
C5' A:U41 4.0 64.0 1.0
O5' A:U41 4.0 61.0 1.0
O3' A:A6 4.1 63.1 1.0
O3' A:G5 4.2 67.1 1.0
C3' A:U41 4.3 66.1 1.0
O5' A:G42 4.3 68.9 1.0
OP2 A:U41 4.3 61.6 1.0
O5' A:A6 4.3 60.9 1.0
C3' A:A6 4.4 62.2 1.0
O5' A:U7 4.4 56.5 1.0
O3' A:A40 4.5 57.8 1.0
C4' A:U41 4.6 65.6 1.0
N2 A:G39 4.7 61.5 1.0
C5' A:G42 4.8 70.4 1.0
OP2 A:G8 4.8 60.2 1.0
TL A:TL116 4.8 0.6 1.0
C5' A:A6 4.9 65.7 1.0

Magnesium binding site 3 out of 9 in 4en5

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Magnesium binding site 3 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:61.7
occ:1.00
 F A:F110 1.8 67.4 1.0
O A:HOH214 2.0 65.9 1.0
O A:HOH215 2.1 60.5 1.0
O A:HOH203 2.1 66.1 1.0
OP1 A:U7 2.2 67.2 1.0
OP2 A:G8 2.4 60.2 1.0
MG A:MG102 2.7 60.4 1.0
MG A:MG104 2.9 72.4 1.0
P A:U7 3.0 56.2 1.0
OP2 A:U7 3.0 59.2 1.0
OP1 A:U41 3.5 61.9 1.0
P A:G8 3.6 62.9 1.0
OP1 A:A6 3.7 65.5 1.0
O5' A:U7 4.0 56.5 1.0
TL A:TL116 4.0 0.6 1.0
OP1 A:G8 4.0 61.5 1.0
OP2 A:A6 4.0 66.5 1.0
OP1 A:G42 4.3 64.8 1.0
O3' A:A6 4.3 63.1 1.0
OP2 A:G42 4.3 62.4 1.0
C5' A:U41 4.4 64.0 1.0
P A:A6 4.4 58.3 1.0
O A:HOH217 4.5 57.6 1.0
O3' A:U7 4.6 61.4 1.0
C3' A:U7 4.6 59.0 1.0
P A:G42 4.7 61.8 1.0
O5' A:G8 4.7 60.5 1.0
P A:U41 4.7 56.5 1.0
O3' A:U41 4.8 66.3 1.0
O A:HOH226 4.8 81.5 1.0
C5' A:U7 4.8 61.2 1.0
O2' A:A40 4.9 56.3 1.0
O3' A:A40 4.9 57.8 1.0
O A:HOH202 5.0 68.2 1.0

Magnesium binding site 4 out of 9 in 4en5

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Magnesium binding site 4 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:72.4
occ:1.00
 F A:F110 1.9 67.4 1.0
O A:HOH214 2.1 65.9 1.0
O A:HOH203 2.2 66.1 1.0
O A:HOH226 2.2 81.5 1.0
OP1 A:G42 2.3 64.8 1.0
OP1 A:A6 2.3 65.5 1.0
MG A:MG103 2.9 61.7 1.0
P A:G42 3.3 61.8 1.0
MG A:MG102 3.5 60.4 1.0
P A:A6 3.5 58.3 1.0
O3' A:U41 3.6 66.3 1.0
OP2 A:A6 3.9 66.5 1.0
OP2 A:G42 4.0 62.4 1.0
OP1 A:U7 4.0 67.2 1.0
O3' A:G5 4.2 67.1 1.0
TL A:TL116 4.3 0.6 1.0
O5' A:G5 4.3 63.3 1.0
C3' A:G5 4.3 72.4 1.0
OP2 A:G5 4.4 67.7 1.0
O A:HOH215 4.7 60.5 1.0
O5' A:G42 4.7 68.9 1.0
OP2 A:U7 4.7 59.2 1.0
O5' A:A6 4.7 60.9 1.0
P A:G5 4.8 64.2 1.0
C3' A:U41 4.8 66.1 1.0
P A:U7 4.9 56.2 1.0
TL A:TL113 4.9 0.6 1.0
OP2 A:G8 4.9 60.2 1.0

Magnesium binding site 5 out of 9 in 4en5

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Magnesium binding site 5 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:78.8
occ:1.00
 O A:HOH216 2.1 77.2 1.0
O A:HOH234 3.0 79.0 1.0
O6 A:G2 3.2 82.3 1.0
N7 A:G2 3.3 78.0 1.0
C6 A:G2 3.8 79.6 1.0
C5 A:G2 3.8 78.4 1.0
C8 A:G2 4.4 79.2 1.0
O A:HOH233 4.9 98.5 1.0

Magnesium binding site 6 out of 9 in 4en5

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Magnesium binding site 6 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:53.5
occ:1.00
 N7 A:G34 2.0 56.9 1.0
O A:HOH208 2.1 67.1 1.0
O A:HOH209 2.1 52.7 1.0
C8 A:G34 2.9 56.4 1.0
TL A:TL115 3.1 0.1 1.0
C5 A:G34 3.1 53.7 1.0
N7 A:A33 3.5 55.1 1.0
C5 A:A33 3.6 55.1 1.0
O6 A:G34 3.6 58.0 1.0
C6 A:G34 3.7 54.5 1.0
C6 A:A33 3.9 53.0 1.0
C8 A:A33 4.0 53.4 1.0
N9 A:G34 4.1 54.8 1.0
N6 A:A33 4.1 51.1 1.0
C4 A:A33 4.1 54.1 1.0
C4 A:G34 4.2 54.9 1.0
N9 A:A33 4.4 53.5 1.0
O A:HOH229 4.5 64.7 1.0
N1 A:A33 4.7 56.1 1.0
OP2 A:G34 4.7 59.2 1.0
O A:HOH230 4.8 61.7 1.0
N7 A:G35 4.8 57.8 1.0
O6 A:G35 4.9 57.3 1.0
N3 A:A33 4.9 53.6 1.0

Magnesium binding site 7 out of 9 in 4en5

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Magnesium binding site 7 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:54.6
occ:1.00
 O A:HOH207 2.1 69.3 1.0
O6 A:G36 2.3 54.7 1.0
O A:HOH229 2.7 64.7 1.0
O A:HOH230 2.8 61.7 1.0
N7 A:G36 3.0 57.3 1.0
C6 A:G36 3.1 56.6 1.0
TL A:TL115 3.2 0.1 1.0
C5 A:G36 3.4 57.2 1.0
O6 A:G35 3.4 57.3 1.0
C6 A:G35 4.0 56.5 1.0
C8 A:G36 4.3 57.5 1.0
N4 A:C37 4.3 59.5 1.0
N1 A:G36 4.5 56.4 1.0
C5 A:G35 4.5 56.4 1.0
N7 A:G35 4.6 57.8 1.0
C4 A:G36 4.8 57.0 1.0
N1 A:G35 4.8 55.8 1.0
N4 A:C26 5.0 58.4 1.0

Magnesium binding site 8 out of 9 in 4en5

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Magnesium binding site 8 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:77.4
occ:1.00
 OP1 A:C50 3.1 88.5 1.0
N7 A:G52 3.3 79.3 1.0
O6 A:G52 3.8 76.1 1.0
C5 A:G52 4.2 77.0 1.0
C8 A:G52 4.2 78.8 1.0
P A:C50 4.3 87.7 1.0
C6 A:G52 4.4 76.5 1.0
O5' A:C50 4.6 76.2 1.0
OP2 A:C50 4.9 72.1 1.0
C5' A:C50 5.0 75.2 1.0

Magnesium binding site 9 out of 9 in 4en5

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Magnesium binding site 9 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg109

b:54.5
occ:1.00
 O A:HOH212 2.1 62.4 1.0
O A:HOH210 2.1 55.4 1.0
O A:HOH211 2.1 55.8 1.0
O A:HOH213 2.1 56.1 1.0
OP2 A:A40 2.3 60.6 1.0
O5' A:A40 2.5 56.7 1.0
P A:A40 2.9 58.3 1.0
C5' A:A40 3.8 58.1 1.0
OP1 A:A40 3.9 59.2 1.0
O4 A:U7 3.9 57.5 1.0
O4' A:A40 4.0 51.2 1.0
O3' A:G39 4.1 57.9 1.0
N1 A:A49 4.2 55.8 1.0
C3' A:G39 4.3 62.7 1.0
C4' A:A40 4.3 55.9 1.0
N6 A:A49 4.4 58.4 1.0
N3 A:C50 4.4 60.0 1.0
C6 A:A49 4.8 58.7 1.0
O2 A:C50 4.8 64.5 1.0
O5' A:G39 4.9 63.7 1.0
C4 A:U7 5.0 55.4 1.0
O A:HOH222 5.0 69.3 1.0

Reference:

A.Ren, K.R.Rajashankar, D.J.Patel. Fluoride Ion Encapsulation By MG2+ Ions and Phosphates in A Fluoride Riboswitch. Nature V. 486 85 2012.
ISSN: ISSN 0028-0836
PubMed: 22678284
DOI: 10.1038/NATURE11152
Page generated: Fri Aug 16 14:32:05 2024

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