Sodium in PDB 5nz3: The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine, PDB code: 5nz3 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)	48.78 / 2.06
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.491, 83.491, 66.071, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 27.4

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Bromine	(Br)	4 atoms

The binding sites of Sodium atom in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine (pdb code 5nz3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine, PDB code: 5nz3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:36.0 occ:1.00 H62 A:A32 2.1 54.0 1.0 O2' A:G29 2.5 29.5 1.0 OP2 A:A30 2.7 43.0 1.0 N6 A:A32 2.9 45.0 1.0 O3' A:G29 2.9 39.3 1.0 H1' A:G29 3.0 38.4 1.0 H61 A:A32 3.1 54.0 1.0 P A:A30 3.2 43.5 1.0 C2' A:G29 3.4 36.9 1.0 H61 A:A33 3.4 68.9 1.0 O A:HOH205 3.5 30.0 1.0 H41 A:C31 3.6 64.6 1.0 C1' A:G29 3.6 32.0 1.0 C3' A:G29 3.7 29.6 1.0 OP1 A:A30 3.8 43.9 1.0 N6 A:A33 3.8 57.4 1.0 H1' A:A5 3.8 43.1 1.0 H62 A:A33 3.9 68.9 1.0 MG A:MG102 3.9 49.4 1.0 C6 A:A32 4.0 35.5 1.0 H2' A:G29 4.2 44.3 1.0 H5 A:C31 4.2 34.4 1.0 N4 A:C31 4.2 53.8 1.0 N7 A:A32 4.3 41.1 1.0 H3' A:G29 4.3 35.5 1.0 N3 A:G29 4.5 31.6 1.0 O2' A:A5 4.5 32.4 1.0 N9 A:G29 4.5 37.5 1.0 C5 A:A32 4.5 33.7 1.0 O4' A:G29 4.7 42.3 1.0 O5' A:A30 4.7 39.5 1.0 H42 A:C31 4.7 64.6 1.0 C6 A:A33 4.7 36.0 1.0 C1' A:A5 4.7 35.9 1.0 H4' A:A5 4.7 42.7 1.0 C4' A:G29 4.7 40.3 1.0 O A:HOH207 4.8 30.0 1.0 C4 A:G29 4.8 35.4 1.0 C5 A:C31 4.8 28.7 1.0 N3 A:A5 4.8 43.2 1.0 H4' A:G29 4.9 48.4 1.0 C4 A:C31 4.9 36.1 1.0 O4' A:A5 5.0 35.6 1.0 N1 A:A33 5.0 36.7 1.0

Sodium binding site 2 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:65.2 occ:1.00 H41 A:C41 3.7 45.9 1.0 HN42 A:CBV39 3.8 75.1 1.0 N7 A:G40 3.8 35.5 1.0 N4 A:CBV39 3.8 62.6 1.0 C4 A:CBV39 4.0 35.2 1.0 O6 A:G40 4.0 33.1 1.0 O4 A:U11 4.0 34.1 1.0 HN41 A:CBV39 4.2 75.1 1.0 C5 A:CBV39 4.2 42.5 1.0 BR A:CBV39 4.3 39.4 1.0 N4 A:C41 4.3 38.2 1.0 C4 A:U11 4.5 41.5 1.0 H42 A:C41 4.5 45.9 1.0 C5 A:G40 4.7 33.2 1.0 C6 A:G40 4.7 37.4 1.0 N3 A:CBV39 4.7 39.6 1.0 C8 A:G40 4.9 37.8 1.0 H3 A:U11 4.9 47.0 1.0 N3 A:U11 5.0 39.1 1.0

Sodium binding site 3 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:30.0 occ:1.00 OP1 A:A8 2.9 29.4 1.0 H5'' A:A8 2.9 46.3 1.0 H5' A:A8 3.5 46.3 1.0 C5' A:A8 3.7 38.5 1.0 P A:A8 4.2 36.6 1.0 O5' A:A8 4.3 36.6 1.0 O3' A:G7 4.6 40.3 1.0 H4' A:A8 4.7 46.7 1.0 C4' A:A8 4.8 39.0 1.0

Sodium binding site 4 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:30.0 occ:1.00 O6 B:G23 2.3 93.5 1.0 C6 B:G23 3.3 94.5 1.0 O6 B:G24 3.5 97.0 1.0 N7 B:G23 3.8 96.5 1.0 C5 B:G23 3.9 95.9 1.0 H41 B:C22 4.0 0.5 1.0 H42 B:C1 4.2 0.5 1.0 H41 B:C1 4.3 0.5 1.0 N4 B:C22 4.4 94.6 1.0 HN42 B:CBV2 4.5 0.2 1.0 N1 B:G23 4.5 94.4 1.0 H42 B:C22 4.6 0.5 1.0 C6 B:G24 4.6 0.6 1.0 N4 B:C1 4.6 88.7 1.0 H1 B:G23 4.7 0.3 1.0 H5 B:C22 4.9 0.9 1.0 C4 B:C22 5.0 92.8 1.0

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