Sodium in PDB 5nef: The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine, PDB code: 5nef 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)	44.19 / 1.91
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	55.700, 55.700, 132.560, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 25.8

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine (pdb code 5nef). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine, PDB code: 5nef:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine


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 G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:56.9 occ:1.00 OP2 A:C18 2.6 31.8 1.0 O A:HOH205 2.6 40.2 1.0 H5 A:C18 2.7 55.4 1.0 H3' A:CBV17 2.9 45.4 1.0 C5 A:C18 3.6 46.1 1.0 O A:HOH230 3.6 59.5 1.0 H6 A:CBV17 3.6 35.0 1.0 C6 A:CBV17 3.7 29.2 1.0 H6 A:C18 3.8 55.1 1.0 C3' A:CBV17 3.8 37.8 1.0 P A:C18 3.9 37.1 1.0 C5 A:CBV17 3.9 34.8 1.0 HO3' A:CBV17 3.9 41.7 1.0 O5' A:CBV17 4.0 30.7 1.0 C6 A:C18 4.1 45.9 1.0 BR A:CBV17 4.1 46.0 1.0 H2' A:CBV17 4.2 39.1 1.0 O5' A:C18 4.3 32.8 1.0 O3' A:CBV17 4.3 34.8 1.0 O A:HOH233 4.3 75.6 1.0 H41 A:C18 4.3 42.0 1.0 N1 A:CBV17 4.4 32.1 1.0 O1P A:CBV17 4.4 29.9 1.0 C2' A:CBV17 4.5 32.6 1.0 C4 A:CBV17 4.6 35.8 1.0 C4 A:C18 4.7 40.1 1.0 C4' A:CBV17 4.8 37.1 1.0 C5' A:CBV17 4.8 30.2 1.0 P A:CBV17 4.8 34.8 1.0 N4 A:C18 4.9 35.0 1.0 H5'1 A:CBV17 4.9 36.2 1.0 C1' A:CBV17 4.9 28.3 1.0

Sodium binding site 2 out of 6 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine


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 G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:63.3 occ:1.00 H22 A:G1 2.6 41.8 1.0 O A:HOH208 2.9 72.1 1.0 H1' A:G2 3.0 43.7 1.0 N2 A:G1 3.4 34.8 1.0 NA A:NA108 3.7 86.1 1.0 C1' A:G2 3.8 36.4 1.0 H21 A:G1 3.9 41.8 1.0 O4' A:G2 3.9 43.1 1.0 HO2' A:G2 4.0 47.0 1.0 O2' A:G2 4.2 39.2 1.0 N3 A:G1 4.3 35.9 1.0 C2 A:G1 4.3 31.3 1.0 HO2' A:G1 4.4 44.4 1.0 H4' A:G2 4.5 65.4 1.0 C2' A:G2 4.7 33.6 1.0 C4' A:G2 4.8 54.5 1.0 N9 A:G2 4.9 33.8 1.0

Sodium binding site 3 out of 6 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine


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 G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:99.5 occ:0.33 O A:HOH221 4.3 28.6 0.3 O A:HOH210 4.5 37.8 1.0

Sodium binding site 4 out of 6 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine


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 G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:59.6 occ:1.00 O6 A:G7 2.8 37.3 1.0 OP2 A:G10 2.9 44.8 1.0 O A:HOH218 3.3 65.8 1.0 N7 A:G7 3.5 35.4 1.0 HN32 A:GAI101 3.6 56.9 1.0 C6 A:G7 3.6 38.7 1.0 O6 A:G6 3.7 32.5 1.0 HN31 A:GAI101 3.8 56.9 1.0 C5 A:G7 3.9 38.5 1.0 H42 A:C12 3.9 64.4 1.0 P A:G10 4.0 49.0 1.0 N3 A:GAI101 4.0 47.4 1.0 O A:HOH209 4.2 47.1 1.0 C6 A:G6 4.2 33.9 1.0 O A:HOH223 4.3 59.8 1.0 OP1 A:G10 4.3 86.0 1.0 H42 A:C13 4.4 47.0 1.0 O5' A:G10 4.5 50.7 1.0 H41 A:C12 4.5 64.4 1.0 N4 A:C12 4.6 53.7 1.0 N7 A:G6 4.6 36.7 1.0 OP2 A:C9 4.6 35.2 1.0 C5 A:G6 4.6 28.6 1.0 C8 A:G7 4.7 34.6 1.0 N1 A:G7 5.0 31.0 1.0

Sodium binding site 5 out of 6 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:0.5 occ:1.00 OP1 A:A8 2.9 37.2 1.0 H41 A:C9 3.0 52.7 1.0 H2' A:G7 3.3 38.2 1.0 HN21 A:GAI101 3.4 43.7 1.0 N1 A:GAI101 3.6 42.0 1.0 N4 A:C9 3.8 43.9 1.0 O2' A:G7 3.9 34.3 1.0 C2' A:G7 4.0 31.8 1.0 N2 A:GAI101 4.1 36.4 1.0 HN1 A:GAI101 4.1 50.5 1.0 H42 A:C9 4.1 52.7 1.0 HO2' A:G7 4.1 41.1 1.0 O A:HOH226 4.2 49.7 1.0 C A:GAI101 4.3 49.8 1.0 H5 A:C9 4.3 45.8 1.0 P A:A8 4.3 37.9 1.0 N3 A:G7 4.5 32.2 1.0 H22 A:G7 4.5 39.1 1.0 O6 A:G10 4.7 38.3 1.0 C4 A:C9 4.8 55.9 1.0 O3' A:G7 4.8 37.4 1.0 HN22 A:GAI101 4.8 43.7 1.0 N2 A:G7 4.9 32.6 1.0 C5 A:C9 4.9 38.2 1.0 C2 A:G7 4.9 32.4 1.0 C3' A:G7 5.0 29.1 1.0

Sodium binding site 6 out of 6 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:86.1 occ:1.00 HO2' A:G2 2.5 47.0 1.0 H1' A:G2 2.9 43.7 1.0 N3 A:G2 3.0 44.1 1.0 O4 A:SO4102 3.1 90.9 1.0 H22 A:G2 3.1 44.2 1.0 O1 A:SO4102 3.2 0.1 1.0 O2' A:G2 3.3 39.2 1.0 H22 A:G1 3.4 41.8 1.0 H21 A:G1 3.4 41.8 1.0 O2 A:C18 3.6 40.0 1.0 C1' A:G2 3.7 36.4 1.0 N2 A:G2 3.7 36.9 1.0 NA A:NA104 3.7 63.3 1.0 S A:SO4102 3.7 0.4 1.0 N2 A:G1 3.7 34.8 1.0 C2 A:G2 3.7 46.7 1.0 H2' A:G2 3.7 40.3 1.0 C2' A:G2 3.8 33.6 1.0 C4 A:G2 4.0 33.4 1.0 O4' A:U3 4.1 39.2 1.0 H1' A:C18 4.1 43.7 1.0 N9 A:G2 4.2 33.8 1.0 H1' A:U3 4.4 48.4 1.0 H21 A:G2 4.5 44.2 1.0 O3 A:SO4102 4.5 0.9 1.0 C2 A:C18 4.6 39.3 1.0 C1' A:U3 4.8 40.3 1.0 O4' A:G2 4.8 43.1 1.0 H5' A:U3 4.8 45.1 1.0 O2 A:SO4102 4.9 0.5 1.0 C2 A:G1 4.9 31.3 1.0 H4' A:U3 5.0 43.4 1.0 C1' A:C18 5.0 36.4 1.0

L.Huang, J.Wang, D.M.J.Lilley. The Structure of the Guanidine-II Riboswitch. Cell Chem Biol V. 24 695 2017.
ISSN: ESSN 2451-9456
PubMed: 28529131
DOI: 10.1016/J.CHEMBIOL.2017.05.014