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Magnesium in PDB 5nzd: The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.

Protein crystallography data

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121., PDB code: 5nzd was solved by L.Huang, J.Wang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.15 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.460, 64.613, 84.292, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 24.5

Other elements in 5nzd:

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. (pdb code 5nzd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121., PDB code: 5nzd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5nzd

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Magnesium binding site 1 out of 9 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:76.1
occ:1.00
 OP2 A:C13 2.5 59.2 1.0
OP2 A:G12 2.6 62.2 1.0
O A:HOH205 2.6 58.0 1.0
P A:C13 3.6 58.3 1.0
OP1 A:C13 3.9 68.1 1.0
P A:G12 3.9 66.2 1.0
O3' A:G12 4.2 62.8 1.0
O3' A:U11 4.3 51.2 1.0
O A:HOH204 4.5 73.5 1.0
O5' A:G12 4.7 67.0 1.0
C3' A:G12 4.8 61.1 1.0
O2' A:U11 4.8 51.0 1.0
OP2 A:G10 4.9 53.3 1.0
O5' A:C13 4.9 55.4 1.0
C5' A:G12 5.0 62.8 1.0

Magnesium binding site 2 out of 9 in 5nzd

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Magnesium binding site 2 out of 9 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:68.1
occ:1.00
 O A:HOH209 2.2 61.0 1.0
O6 A:G40 3.3 56.7 1.0
N4 A:C41 3.7 62.3 1.0
O4 A:U11 4.0 50.3 1.0
N7 A:G40 4.1 59.0 1.0
C6 A:G40 4.2 51.8 1.0
C4 A:U11 4.2 50.1 1.0
O6 A:G12 4.3 49.2 1.0
C5 A:G40 4.5 51.4 1.0
N4 A:CBV39 4.6 54.7 1.0
C5 A:U11 4.6 54.6 1.0
N3 A:U11 4.7 49.4 1.0
C4 A:C41 4.8 57.8 1.0
C4 A:CBV39 5.0 54.2 1.0

Magnesium binding site 3 out of 9 in 5nzd

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Magnesium binding site 3 out of 9 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:82.1
occ:1.00
 O6 A:G10 3.9 51.2 1.0
N7 A:G9 4.0 53.9 1.0
O2 A:U11 4.3 60.7 1.0
N7 A:G10 4.3 50.4 1.0
O6 A:G9 4.4 51.6 1.0
O A:HOH205 4.5 58.0 1.0
N7 A:G14 4.6 48.2 1.0
C6 A:G10 4.7 49.7 1.0
N4 A:C15 4.7 47.9 1.0
C5 A:G9 4.7 50.9 1.0
C6 A:G9 4.9 51.4 1.0
C5 A:G10 4.9 54.9 1.0
C8 A:G9 4.9 54.4 1.0

Magnesium binding site 4 out of 9 in 5nzd

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Magnesium binding site 4 out of 9 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:85.9
occ:1.00
 O A:HOH208 2.8 61.2 1.0
N7 A:G3 3.7 58.0 1.0
N7 A:G4 4.2 48.3 1.0
O6 A:G4 4.2 47.6 1.0
O6 A:G3 4.4 47.5 1.0
C5 A:G3 4.5 52.3 1.0
C8 A:G3 4.5 51.6 1.0
C6 A:G3 4.7 47.4 1.0
BR A:CBV2 4.8 0.7 1.0
N4 A:CBV2 4.8 60.9 1.0
C6 A:G4 4.9 46.7 1.0
C5 A:G4 4.9 49.3 1.0
C5 A:CBV2 4.9 89.4 1.0
C4 A:CBV2 4.9 66.5 1.0

Magnesium binding site 5 out of 9 in 5nzd

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Magnesium binding site 5 out of 9 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:67.0
occ:1.00
 OP2 A:C31 2.1 0.7 1.0
OP2 A:A30 2.5 82.8 1.0
O A:HOH203 2.5 71.3 1.0
P A:C31 3.3 0.1 1.0
OP2 A:A32 3.5 0.5 1.0
O5' A:C31 3.6 95.8 1.0
N7 A:A32 3.9 74.1 1.0
P A:A30 4.0 83.6 1.0
OP1 A:C31 4.1 0.6 1.0
C5 A:C31 4.2 85.0 1.0
C6 A:C31 4.4 89.8 1.0
C8 A:A32 4.5 81.2 1.0
O3' A:A30 4.6 0.0 1.0
O5' A:A30 4.7 94.3 1.0
OP1 A:A30 4.9 91.5 1.0
C5' A:A30 4.9 0.5 1.0
C3' A:A30 4.9 0.0 1.0
O3' A:G29 4.9 75.7 1.0
P A:A32 4.9 0.2 1.0

Magnesium binding site 6 out of 9 in 5nzd

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Magnesium binding site 6 out of 9 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:47.1
occ:1.00
 OP2 B:C31 1.8 63.1 1.0
OP2 B:A30 1.9 66.3 1.0
O B:HOH207 2.0 50.1 1.0
O B:HOH210 2.3 61.4 1.0
O B:HOH211 2.3 51.9 1.0
O B:HOH206 2.4 49.6 1.0
P B:C31 3.1 62.4 1.0
P B:A30 3.3 57.8 1.0
O5' B:C31 3.5 56.0 1.0
O5' B:A30 4.0 60.4 1.0
OP1 B:A30 4.0 57.5 1.0
OP1 B:C31 4.0 71.6 1.0
C5 B:C31 4.2 52.8 1.0
O3' B:A30 4.3 63.2 1.0
C5' B:A30 4.3 61.0 1.0
O3' B:G29 4.3 49.0 1.0
C6 B:C31 4.3 58.9 1.0
OP2 B:A32 4.4 57.1 1.0
N7 B:A32 4.5 48.7 1.0
C3' B:A30 4.5 58.6 1.0
C5' B:C31 4.9 58.4 1.0

Magnesium binding site 7 out of 9 in 5nzd

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Magnesium binding site 7 out of 9 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:81.0
occ:1.00
 O B:HOH208 2.5 48.8 1.0
N7 B:G3 4.6 50.8 1.0
O B:HOH214 4.7 50.9 1.0
O6 B:G4 5.0 61.0 1.0

Magnesium binding site 8 out of 9 in 5nzd

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Magnesium binding site 8 out of 9 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:77.6
occ:1.00
 O6 B:G10 3.7 57.6 1.0
N7 B:G9 3.9 50.9 1.0
N7 B:G14 4.2 45.0 1.0
O6 B:G9 4.4 43.4 1.0
N7 B:G10 4.4 62.0 1.0
O2 B:U11 4.4 48.7 1.0
C6 B:G10 4.6 51.9 1.0
N4 B:C15 4.6 43.6 1.0
C5 B:G9 4.7 49.2 1.0
C8 B:G9 4.8 46.9 1.0
C5 B:G10 4.8 59.5 1.0
C6 B:G9 4.9 46.1 1.0
C8 B:G14 4.9 47.1 1.0

Magnesium binding site 9 out of 9 in 5nzd

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Magnesium binding site 9 out of 9 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:80.1
occ:1.00
 O B:HOH215 2.2 53.6 1.0
O6 B:G23 3.4 50.4 1.0
N7 B:G23 3.4 59.9 1.0
O6 B:G24 3.9 53.4 1.0
C6 B:G23 3.9 53.4 1.0
C5 B:G23 4.0 55.2 1.0
C8 B:G23 4.5 49.9 1.0
N4 B:C22 4.8 48.6 1.0
N7 B:G24 4.8 57.2 1.0
C6 B:G24 4.9 54.2 1.0
N4 B:C1 5.0 72.9 1.0

Reference:

L.Huang, J.Wang, T.J.Wilson, D.M.J.Lilley. Structure of the Guanidine III Riboswitch. Cell Chem Biol V. 24 1407 2017.
ISSN: ESSN 2451-9456
PubMed: 28988949
DOI: 10.1016/J.CHEMBIOL.2017.08.021
Page generated: Tue Aug 12 16:42:09 2025

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