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

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine, PDB code: 5neq 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)	38.66 / 1.69
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	55.463, 55.463, 130.276, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 25.2

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine 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 Aminoguanidine (pdb code 5neq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine, PDB code: 5neq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine


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 Aminoguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:62.1 occ:1.00 O A:HOH232 2.4 49.1 1.0 H41 A:C15 2.7 39.5 1.0 O A:HOH201 2.8 55.1 1.0 H41 A:C14 3.4 40.5 1.0 N4 A:C15 3.5 32.9 1.0 H42 A:C15 3.8 39.5 1.0 H5 A:C14 3.9 37.2 1.0 N4 A:C14 3.9 33.8 1.0 H5 A:C15 4.0 42.9 1.0 H62 A:A16 4.1 38.6 1.0 C5 A:C14 4.3 31.0 1.0 H42 A:C14 4.4 40.5 1.0 C4 A:C14 4.4 31.1 1.0 C4 A:C15 4.5 30.8 1.0 H61 A:A16 4.6 38.6 1.0 C5 A:C15 4.6 35.7 1.0 N6 A:A16 4.6 32.1 1.0 O A:HOH202 4.7 57.0 1.0 O4 A:SO4103 4.8 0.1 1.0

Sodium binding site 2 out of 7 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine


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 Aminoguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:57.8 occ:1.00 N7 A:G2 3.4 36.0 1.0 N7 A:G1 3.8 31.7 1.0 H8 A:G2 4.1 59.2 1.0 C8 A:G2 4.2 49.3 1.0 OP2 A:G2 4.3 38.4 1.0 C8 A:G1 4.3 39.0 1.0 C5 A:G1 4.4 32.9 1.0 O6 A:G2 4.5 36.0 1.0 H8 A:G1 4.5 46.9 1.0 H3' A:G1 4.5 40.7 1.0 C5 A:G2 4.5 35.9 1.0 O6 A:G1 4.7 33.2 1.0 HO5' A:G1 4.7 58.6 1.0 C6 A:G1 4.7 39.2 1.0 O5' A:G1 4.9 48.8 1.0 C6 A:G2 4.9 37.0 1.0

Sodium binding site 3 out of 7 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine


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 Aminoguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:62.9 occ:1.00 O A:HOH210 3.4 56.0 1.0 O A:HOH213 3.6 35.5 1.0 O A:HOH204 3.7 40.2 1.0

Sodium binding site 4 out of 7 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine


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 Aminoguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:0.9 occ:1.00 H5 A:C13 2.6 40.4 1.0 OP2 A:C13 2.7 47.8 1.0 OP2 A:C12 2.9 47.9 1.0 H3' A:C12 3.2 63.1 1.0 C5 A:C13 3.4 33.7 1.0 O5' A:C12 3.6 53.7 1.0 H6 A:C13 3.8 41.8 1.0 P A:C12 3.8 55.4 1.0 P A:C13 4.0 48.5 1.0 C6 A:C13 4.1 34.8 1.0 H41 A:C13 4.1 44.6 1.0 C3' A:C12 4.1 52.6 1.0 C6 A:C12 4.2 43.6 1.0 C5 A:C12 4.2 49.7 1.0 H6 A:C12 4.2 52.4 1.0 H5 A:C12 4.3 59.6 1.0 O5' A:C13 4.4 39.8 1.0 O A:HOH232 4.5 49.1 1.0 C4 A:C13 4.5 33.6 1.0 O3' A:C12 4.5 47.5 1.0 N4 A:C13 4.7 37.2 1.0 OP1 A:C12 4.7 65.7 1.0 H3' A:A11 4.7 74.5 1.0 N1 A:C12 4.7 46.2 1.0 H2' A:C12 4.7 53.6 1.0 C5' A:C12 4.8 43.0 1.0 C4 A:C12 4.8 60.7 1.0 C2' A:C12 5.0 44.7 1.0 H5'' A:C12 5.0 51.6 1.0

Sodium binding site 5 out of 7 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine


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 Aminoguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:0.1 occ:1.00 OP1 A:A8 2.4 35.3 1.0 H41 A:C9 2.7 49.7 1.0 N7 A:A8 3.1 37.1 1.0 HN42 A:AGU101 3.1 53.3 1.0 H5 A:C9 3.4 48.1 1.0 N4 A:AGU101 3.4 44.4 1.0 N4 A:C9 3.5 41.4 1.0 P A:A8 3.6 37.7 1.0 H8 A:A8 3.6 49.1 1.0 C8 A:A8 3.7 40.9 1.0 H62 A:A8 3.8 55.1 1.0 HN41 A:AGU101 3.9 53.3 1.0 H42 A:C9 4.0 49.7 1.0 OP2 A:A8 4.1 34.7 1.0 C5 A:C9 4.1 40.1 1.0 C5 A:A8 4.1 33.7 1.0 C4 A:C9 4.2 33.2 1.0 N1 A:AGU101 4.4 38.9 1.0 H2' A:G7 4.4 42.8 1.0 N6 A:A8 4.4 45.9 1.0 O5' A:A8 4.5 33.9 1.0 N3 A:AGU101 4.5 40.7 1.0 C6 A:A8 4.7 43.0 1.0 O3' A:G7 4.8 32.4 1.0 N9 A:A8 4.9 40.0 1.0 HN1 A:AGU101 4.9 46.7 1.0 C A:AGU101 4.9 50.0 1.0 HO2' A:G7 5.0 46.5 1.0

Sodium binding site 6 out of 7 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine


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 Aminoguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:59.5 occ:1.00 H22 A:G1 2.7 42.5 1.0 H1' A:G2 3.2 39.0 1.0 O A:HOH220 3.3 45.6 1.0 N2 A:G1 3.5 35.4 1.0 O A:HOH209 3.6 51.2 1.0 HO2' A:G2 3.9 45.0 1.0 H21 A:G1 4.0 42.5 1.0 C1' A:G2 4.1 32.5 1.0 O2' A:G2 4.2 37.5 1.0 O4' A:G2 4.2 36.4 1.0 C2 A:G1 4.5 30.8 1.0 N3 A:G1 4.5 32.7 1.0 H4' A:G2 4.7 40.9 1.0 C2' A:G2 4.8 32.5 1.0 HO2' A:G1 4.9 46.6 1.0

Sodium binding site 7 out of 7 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Aminoguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na110 b:0.2 occ:1.00 O A:HOH233 2.3 78.9 1.0 OP2 A:G10 2.8 42.8 1.0 O6 A:G7 3.0 34.0 1.0 N7 A:G7 3.1 53.9 1.0 HN21 A:AGU101 3.2 82.3 1.0 HN22 A:AGU101 3.6 82.3 1.0 N2 A:AGU101 3.6 68.6 1.0 C6 A:G7 3.7 36.9 1.0 C5 A:G7 3.7 38.8 1.0 O6 A:G6 3.8 35.6 1.0 OP2 A:C9 4.1 35.9 1.0 P A:G10 4.2 50.0 1.0 C8 A:G7 4.2 31.9 1.0 C6 A:G6 4.2 32.9 1.0 H42 A:C12 4.3 77.9 1.0 OP1 A:C9 4.5 88.1 1.0 N7 A:G6 4.5 29.7 1.0 H8 A:G7 4.5 38.3 1.0 C5 A:G6 4.5 32.2 1.0 P A:C9 4.7 44.8 1.0 OP1 A:G10 4.7 64.0 1.0 C A:AGU101 4.8 50.0 1.0 H42 A:C13 4.8 44.6 1.0 H3' A:C9 4.8 47.7 1.0 O5' A:G10 4.9 57.6 1.0 N4 A:C12 5.0 64.9 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