Atomistry » Magnesium » PDB 3ism-3jaw » 3ivn
Atomistry »
  Magnesium »
    PDB 3ism-3jaw »
      3ivn »

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

Go back to Magnesium Binding Sites List in 3ivn
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

Go back to Magnesium Binding Sites List in 3ivn
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

Go back to Magnesium Binding Sites List in 3ivn
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

Go back to Magnesium Binding Sites List in 3ivn
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

Go back to Magnesium Binding Sites List in 3ivn
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

Go back to Magnesium Binding Sites List in 3ivn
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

Go back to Magnesium Binding Sites List in 3ivn
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

Go back to Magnesium Binding Sites List in 3ivn
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

Go back to Magnesium Binding Sites List in 3ivn
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: Wed Aug 14 16:19:41 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy