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

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine, PDB code: 5nex 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)	45.42 / 1.72
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	55.639, 55.639, 135.927, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 23.3

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine 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 Agmatine (pdb code 5nex). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine, PDB code: 5nex:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine


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 Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:42.3 occ:1.00 N3 A:A16 2.8 24.6 1.0 H1' A:A16 2.9 31.8 1.0 O2' A:A16 2.9 27.6 1.0 H2' A:A16 3.2 26.9 1.0 HO2' A:A16 3.2 33.1 1.0 C2' A:A16 3.3 22.4 1.0 O4' A:CBV17 3.5 29.1 1.0 C1' A:A16 3.5 26.5 1.0 H2 A:A16 3.5 31.2 1.0 H1' A:CBV17 3.6 30.8 1.0 C2 A:A16 3.6 26.0 1.0 C4 A:A16 3.8 28.9 1.0 H22 A:G4 3.8 38.4 1.0 C1' A:CBV17 4.0 25.7 1.0 O A:HOH214 4.0 64.9 1.0 N3 A:G4 4.0 36.2 1.0 N9 A:A16 4.1 26.5 1.0 N2 A:G4 4.2 32.0 1.0 H1' A:G4 4.3 37.2 1.0 N1 A:CBV17 4.3 26.0 1.0 C2 A:G4 4.3 28.9 1.0 H6 A:CBV17 4.4 29.1 1.0 C6 A:CBV17 4.5 24.3 1.0 H21 A:G4 4.7 38.4 1.0 C4' A:CBV17 4.7 28.1 1.0 O4' A:A16 4.7 26.8 1.0 H5'2 A:CBV17 4.8 30.9 1.0 C4 A:G4 4.8 37.4 1.0 C3' A:A16 4.8 25.7 1.0 H4' A:CBV17 4.8 33.7 1.0 N1 A:A16 5.0 24.3 1.0

Sodium binding site 2 out of 8 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine


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 Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:44.5 occ:0.33 OP1 A:G6 2.8 30.2 1.0 H5'' A:G6 2.9 33.9 1.0 NA A:NA105 3.2 41.8 0.3 H5' A:G6 3.3 33.9 1.0 C5' A:G6 3.5 28.2 1.0 P A:G6 4.0 31.1 1.0 O5' A:G6 4.2 28.6 1.0 O3' A:G5 4.2 26.5 1.0 HO2' A:G5 4.6 33.3 1.0 H4' A:G6 4.7 31.1 1.0 C4' A:G6 4.8 25.9 1.0

Sodium binding site 3 out of 8 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine


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 Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:50.4 occ:0.33 O2P A:CBV17 2.9 26.4 1.0 H5'1 A:CBV17 2.9 30.9 1.0 H5'2 A:CBV17 3.5 30.9 1.0 C5' A:CBV17 3.6 25.7 1.0 P A:CBV17 4.1 30.6 1.0 NA A:NA106 4.1 58.0 0.3 O A:HOH208 4.2 46.0 1.0 O5' A:CBV17 4.3 25.7 1.0 O3P A:CBV17 4.4 61.3 1.0 O3' A:A16 4.7 29.0 1.0 H4' A:CBV17 4.7 33.7 1.0 C4' A:CBV17 4.8 28.1 1.0

Sodium binding site 4 out of 8 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine


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 Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:43.3 occ:1.00 O2' A:CBV17 2.8 30.4 1.0 H5' A:C18 2.9 40.4 1.0 HO2' A:CBV17 3.2 36.5 1.0 O3' A:CBV17 3.4 28.1 1.0 H4' A:CBV17 3.5 33.7 1.0 C5' A:C18 3.8 33.6 1.0 H5'' A:C18 3.9 40.4 1.0 HO3' A:CBV17 3.9 33.8 1.0 C2' A:CBV17 3.9 25.2 1.0 C3' A:CBV17 4.0 25.9 1.0 OP1 A:C18 4.2 30.2 1.0 C4' A:CBV17 4.2 28.1 1.0 P A:C18 4.4 33.2 1.0 H2' A:CBV17 4.5 30.3 1.0 O5' A:C18 4.5 31.4 1.0 H4' A:C18 4.7 39.3 1.0 C4' A:C18 4.8 32.7 1.0 C1' A:CBV17 5.0 25.7 1.0 H3' A:CBV17 5.0 31.1 1.0 H1' A:CBV17 5.0 30.8 1.0

Sodium binding site 5 out of 8 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine


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 Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:41.8 occ:0.33 HO2' A:G5 2.1 33.3 1.0 H5' A:G6 2.7 33.9 1.0 O2' A:G5 2.8 27.7 1.0 NA A:NA102 3.2 44.5 0.3 O3' A:G5 3.2 26.5 1.0 C5' A:G6 3.6 28.2 1.0 H4' A:G5 3.8 36.9 1.0 H5'' A:G6 3.8 33.9 1.0 C2' A:G5 3.9 24.6 1.0 OP1 A:G6 4.0 30.2 1.0 C3' A:G5 4.0 26.6 1.0 P A:G6 4.1 31.1 1.0 O5' A:G6 4.3 28.6 1.0 H2' A:G5 4.3 29.5 1.0 C4' A:G5 4.4 30.8 1.0 H4' A:G6 4.5 31.1 1.0 C4' A:G6 4.6 25.9 1.0 H3' A:G5 4.9 32.0 1.0 O4' A:G6 5.0 28.5 1.0

Sodium binding site 6 out of 8 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine


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 Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:58.0 occ:0.33 HO2' A:A16 2.4 33.1 1.0 H5'2 A:CBV17 2.8 30.9 1.0 O2' A:A16 2.9 27.6 1.0 O3P A:CBV17 3.5 61.3 1.0 O3' A:A16 3.5 29.0 1.0 H4' A:A16 3.7 33.8 1.0 C5' A:CBV17 3.8 25.7 1.0 C2' A:A16 4.1 22.4 1.0 H5'1 A:CBV17 4.1 30.9 1.0 NA A:NA103 4.1 50.4 0.3 C3' A:A16 4.2 25.7 1.0 O2P A:CBV17 4.3 26.4 1.0 P A:CBV17 4.4 30.6 1.0 O5' A:CBV17 4.4 25.7 1.0 C4' A:A16 4.4 28.1 1.0 H4' A:CBV17 4.5 33.7 1.0 H2' A:A16 4.6 26.9 1.0 C4' A:CBV17 4.6 28.1 1.0 O4' A:CBV17 4.8 29.1 1.0

Sodium binding site 7 out of 8 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine


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 Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:48.7 occ:1.00 O2' A:G6 2.9 30.5 1.0 H5' A:G7 3.0 35.7 1.0 HO2' A:G6 3.2 36.6 1.0 O3' A:G6 3.4 32.5 1.0 H4' A:G6 3.4 31.1 1.0 C5' A:G7 3.8 29.7 1.0 H5'' A:G7 3.9 35.7 1.0 C2' A:G6 4.0 26.7 1.0 C3' A:G6 4.1 28.4 1.0 C4' A:G6 4.2 25.9 1.0 OP1 A:G7 4.3 33.5 1.0 P A:G7 4.4 32.9 1.0 O5' A:G7 4.5 29.5 1.0 H2' A:G6 4.5 32.1 1.0 H4' A:G7 4.7 37.6 1.0 C4' A:G7 4.9 31.4 1.0 H5'' A:G6 5.0 33.9 1.0 H3' A:G6 5.0 34.1 1.0

Sodium binding site 8 out of 8 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:88.9 occ:1.00 H1' A:G5 2.7 38.7 1.0 N3 A:G5 2.9 33.0 1.0 O2' A:G5 3.1 27.7 1.0 H22 A:G5 3.2 42.5 1.0 C1' A:G5 3.4 32.2 1.0 C2' A:G5 3.6 24.6 1.0 H2' A:G5 3.6 29.5 1.0 C2 A:G5 3.7 30.3 1.0 N2 A:G5 3.8 35.4 1.0 C4 A:G5 3.8 23.6 1.0 H21 A:G4 3.8 38.4 1.0 HO2' A:G5 3.9 33.3 1.0 O2 A:C15 3.9 29.5 1.0 H22 A:G4 3.9 38.4 1.0 N9 A:G5 4.0 28.4 1.0 N2 A:G4 4.0 32.0 1.0 O4' A:G6 4.4 28.5 1.0 H1' A:C15 4.5 30.2 1.0 O4' A:G5 4.6 34.3 1.0 H21 A:G5 4.6 42.5 1.0 H1' A:G6 4.7 32.9 1.0 C2 A:C15 4.9 25.1 1.0 C2 A:G4 5.0 28.9 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