Atomistry » Magnesium » PDB 5nol-5o5w » 5nzd
Atomistry »
  Magnesium »
    PDB 5nol-5o5w »
      5nzd »

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

Go back to Magnesium Binding Sites List in 5nzd
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

Go back to Magnesium Binding Sites List in 5nzd
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

Go back to Magnesium Binding Sites List in 5nzd
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

Go back to Magnesium Binding Sites List in 5nzd
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

Go back to Magnesium Binding Sites List in 5nzd
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

Go back to Magnesium Binding Sites List in 5nzd
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

Go back to Magnesium Binding Sites List in 5nzd
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

Go back to Magnesium Binding Sites List in 5nzd
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

Go back to Magnesium Binding Sites List in 5nzd
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: Sun Sep 29 23:43:37 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