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Magnesium in PDB 3ivn: Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon

Protein crystallography data

The structure of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon, PDB code: 3ivn was solved by V.Delfosse, P.Dagenais, D.Chausse, G.Di Tomasso, P.Legault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.04 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.930, 46.330, 87.240, 90.00, 120.04, 90.00
R / Rfree (%) 22.7 / 27.7

Other elements in 3ivn:

The structure of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon (pdb code 3ivn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon, PDB code: 3ivn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3ivn

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Magnesium binding site 1 out of 9 in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:19.5
occ:1.00
 O6 A:G6 3.0 21.8 1.0
O6 A:G71 3.0 21.6 1.0
O4 A:U72 3.1 21.9 1.0
O6 A:G5 3.2 21.4 1.0
O A:HOH144 3.2 19.4 1.0
N4 A:C7 3.7 21.4 1.0
C6 A:G5 3.9 21.2 1.0
C4 A:U72 4.0 21.5 1.0
N3 A:U72 4.0 21.2 1.0
C6 A:G6 4.1 21.6 1.0
C6 A:G71 4.2 20.8 1.0
N7 A:G6 4.4 21.7 1.0
C5 A:G5 4.5 21.3 1.0
N4 A:C73 4.5 21.6 1.0
N7 A:G5 4.6 21.4 1.0
O6 A:G70 4.6 20.5 1.0
C5 A:G6 4.6 21.9 1.0
C4 A:C7 4.8 21.5 1.0
N1 A:G5 4.9 21.4 1.0
C5 A:G71 5.0 20.3 1.0

Magnesium binding site 2 out of 9 in 3ivn

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Magnesium binding site 2 out of 9 in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:15.1
occ:1.00
 O3' A:U13 2.8 18.2 1.0
O2' A:U13 2.8 18.5 1.0
O6 A:G39 2.9 18.4 1.0
OP2 A:A14 3.1 18.4 1.0
P A:A14 3.5 19.1 1.0
C2' A:U13 3.7 18.1 1.0
C3' A:U13 3.9 18.2 1.0
C6 A:G39 4.0 18.3 1.0
C1' A:U13 4.1 17.8 1.0
O5' A:A14 4.1 17.6 1.0
O2 A:U13 4.2 18.2 1.0
N6 A:A12 4.2 18.3 1.0
N6 A:A64 4.4 18.9 1.0
OP2 A:A15 4.4 18.4 1.0
C6 A:A12 4.4 18.5 1.0
N7 A:A12 4.5 18.6 1.0
C5 A:A12 4.5 18.2 1.0
N4 A:C65 4.5 18.4 1.0
N7 A:G39 4.6 18.2 1.0
C5 A:G39 4.7 18.1 1.0
OP1 A:A14 4.8 18.1 1.0
C4' A:U13 4.9 18.5 1.0
O4' A:U13 5.0 18.2 1.0

Magnesium binding site 3 out of 9 in 3ivn

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Magnesium binding site 3 out of 9 in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:17.9
occ:1.00
 O A:HOH133 2.8 18.2 1.0
OP1 A:A15 2.8 17.6 1.0
O A:HOH141 2.8 18.6 1.0
O A:HOH131 3.5 16.6 1.0
O A:HOH130 3.7 16.8 1.0
N7 A:G63 4.0 20.1 1.0
C5 A:U62 4.3 21.1 1.0
P A:A15 4.3 17.8 1.0
O6 A:G63 4.7 19.0 1.0
C4 A:U62 4.7 21.0 1.0
O4 A:U62 4.8 21.2 1.0
C6 A:U62 4.8 21.1 1.0
C8 A:G63 4.9 20.0 1.0
O5' A:A15 4.9 17.3 1.0
OP2 A:G63 4.9 18.8 1.0
N7 A:A15 5.0 18.5 1.0
C5 A:G63 5.0 19.7 1.0

Magnesium binding site 4 out of 9 in 3ivn

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Magnesium binding site 4 out of 9 in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:18.7
occ:1.00
 N7 A:G37 2.9 19.2 1.0
O4 A:U38 3.1 20.5 1.0
O6 A:G37 3.4 18.3 1.0
C5 A:G37 3.7 18.8 1.0
N3 A:U38 3.8 19.4 1.0
C4 A:U38 3.8 19.8 1.0
N7 A:G36 3.8 18.8 1.0
C6 A:G37 3.9 18.4 1.0
C8 A:G37 3.9 19.1 1.0
C8 A:G36 4.2 19.2 1.0
OP2 A:G36 4.5 20.5 1.0
C5 A:G36 4.6 18.9 1.0
C2 A:U38 5.0 19.8 1.0
C4 A:G37 5.0 18.5 1.0

Magnesium binding site 5 out of 9 in 3ivn

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Magnesium binding site 5 out of 9 in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:17.7
occ:1.00
 O A:HOH149 3.1 20.2 1.0
N2 A:G10 3.3 19.1 1.0
O A:HOH143 3.6 17.6 1.0
C1' A:U11 3.6 19.6 1.0
O4' A:U11 3.9 20.1 1.0
C1' A:U69 4.1 20.2 1.0
O2' A:U11 4.1 20.4 1.0
O2 A:U11 4.2 18.8 1.0
C2 A:G10 4.3 18.9 1.0
O4' A:U69 4.3 20.4 1.0
N3 A:G10 4.4 19.2 1.0
N1 A:U11 4.5 18.9 1.0
C2' A:U11 4.5 19.8 1.0
O2 A:C68 4.6 19.0 1.0
N1 A:U69 4.7 20.0 1.0
C2 A:U11 4.7 18.6 1.0
O2 A:U69 4.8 19.6 1.0
O2' A:U69 4.9 20.5 1.0
C4' A:U11 4.9 20.6 1.0
C2 A:U69 5.0 19.4 1.0

Magnesium binding site 6 out of 9 in 3ivn

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Magnesium binding site 6 out of 9 in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:19.7
occ:1.00
 O6 B:G6 2.9 20.8 1.0
O4 B:U72 3.0 19.5 1.0
O6 B:G5 3.1 22.2 1.0
O6 B:G71 3.2 19.4 1.0
O B:HOH122 3.6 17.4 1.0
C4 B:U72 3.9 19.2 1.0
C6 B:G5 3.9 21.3 1.0
N4 B:C7 3.9 19.9 1.0
C6 B:G6 4.0 20.6 1.0
N3 B:U72 4.1 19.4 1.0
N4 B:C73 4.1 20.3 1.0
C6 B:G71 4.3 19.0 1.0
N7 B:G6 4.5 20.6 1.0
C5 B:G6 4.7 20.3 1.0
C5 B:G5 4.7 21.5 1.0
N1 B:G5 4.7 21.0 1.0
N7 B:G71 4.8 18.9 1.0
N7 B:G5 4.9 21.3 1.0
C5 B:G71 4.9 19.0 1.0
C4 B:C7 5.0 20.0 1.0

Magnesium binding site 7 out of 9 in 3ivn

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Magnesium binding site 7 out of 9 in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:25.5
occ:0.92
 OP2 B:A14 2.6 30.1 1.0
O6 B:G39 2.8 25.5 1.0
N4 B:C65 3.3 23.5 1.0
O2' B:U13 3.3 26.3 1.0
N6 B:A64 3.7 22.8 1.0
C6 B:G39 4.0 24.7 1.0
P B:A14 4.1 30.3 1.0
N6 B:A12 4.4 21.3 1.0
C4 B:C65 4.5 23.0 1.0
C2' B:U13 4.6 26.5 1.0
C6 B:A12 4.7 21.9 1.0
O2 B:U13 4.7 27.4 1.0
O5' B:A14 4.8 28.3 1.0
C6 B:A64 4.8 23.1 1.0
C5 B:G39 4.8 25.0 1.0
N7 B:G39 4.9 25.1 1.0
OP2 B:A15 4.9 27.6 1.0
N1 B:G39 4.9 24.3 1.0
C1' B:U13 4.9 27.1 1.0

Magnesium binding site 8 out of 9 in 3ivn

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Magnesium binding site 8 out of 9 in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:25.7
occ:0.94
 O B:HOH116 2.9 24.1 1.0
O B:HOH115 3.3 25.0 1.0
N7 B:G63 3.4 22.6 1.0
O B:HOH124 3.6 23.4 1.0
C5 B:U62 3.6 23.9 1.0
OP1 B:A15 3.7 25.6 1.0
C4 B:U62 4.0 23.4 1.0
O B:HOH131 4.1 24.2 1.0
O4 B:U62 4.2 23.3 1.0
C6 B:U62 4.2 23.9 1.0
O6 B:G63 4.3 23.2 1.0
C8 B:G63 4.3 22.7 1.0
C5 B:G63 4.4 22.4 1.0
OP2 B:G63 4.8 22.8 1.0
C6 B:G63 4.8 22.6 1.0
OP2 B:U62 4.8 24.5 1.0
N3 B:U62 4.9 23.1 1.0

Magnesium binding site 9 out of 9 in 3ivn

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Magnesium binding site 9 out of 9 in the Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the U65C Mutant A-Riboswitch Aptamer From the Bacillus Subtilis Pbue Operon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:36.0
occ:1.00
 N6 B:A50 3.3 34.7 1.0
C4 B:G29 3.5 42.1 1.0
N3 B:G29 3.6 41.5 1.0
C5 B:G29 3.7 41.6 1.0
N1 B:A58 3.8 46.0 1.0
C2 B:G29 3.9 39.8 1.0
N9 B:G29 3.9 44.1 1.0
C2 B:A58 4.0 45.8 1.0
C6 B:G29 4.0 40.1 1.0
N1 B:G29 4.1 38.5 1.0
C2' B:G29 4.1 46.6 1.0
N7 B:G29 4.2 42.5 1.0
C8 B:G29 4.3 43.8 1.0
N6 B:A49 4.4 28.7 1.0
C6 B:A50 4.5 32.5 1.0
C1' B:G29 4.5 46.3 1.0
N2 B:G29 4.6 39.1 1.0
O6 B:G29 4.8 39.5 1.0
O4 B:U59 4.8 31.6 1.0
C6 B:A58 4.9 47.2 1.0
O2' B:G29 4.9 46.9 1.0
OP1 B:U30 5.0 49.6 1.0

Reference:

V.Delfosse, P.Bouchard, E.Bonneau, P.Dagenais, J.F.Lemay, D.A.Lafontaine, P.Legault. Riboswitch Structure: An Internal Residue Mimicking the Purine Ligand. Nucleic Acids Res. V. 38 2057 2010.
ISSN: ISSN 0305-1048
PubMed: 20022916
DOI: 10.1093/NAR/GKP1080
Page generated: Sun Aug 10 22:43:10 2025

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