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

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Methylguanidine, PDB code: 5nep 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)	27.75 / 1.60
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	55.500, 55.500, 132.379, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 21.8

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Methylguanidine 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 Methylguanidine (pdb code 5nep). 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 G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Methylguanidine, PDB code: 5nep:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop 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 G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Methylguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:36.7 occ:0.33 HO2' A:A16 2.3 33.5 1.0 H5'2 A:CBV17 2.7 32.2 1.0 O2' A:A16 2.9 27.9 1.0 O3P A:CBV17 3.3 45.5 1.0 O3' A:A16 3.4 34.5 1.0 C5' A:CBV17 3.7 26.9 1.0 H4' A:A16 3.8 31.8 1.0 O A:HOH202 4.0 31.4 0.3 C2' A:A16 4.0 27.6 1.0 H5'1 A:CBV17 4.0 32.2 1.0 O2P A:CBV17 4.1 26.5 1.0 C3' A:A16 4.1 26.8 1.0 P A:CBV17 4.3 27.1 1.0 O5' A:CBV17 4.4 25.9 1.0 H4' A:CBV17 4.4 33.7 1.0 C4' A:A16 4.5 26.5 1.0 H2' A:A16 4.5 33.1 1.0 C4' A:CBV17 4.5 28.1 1.0 O4' A:CBV17 4.8 27.9 1.0

Sodium binding site 2 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop 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 G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Methylguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:80.9 occ:0.33 HO2' A:G5 2.1 37.9 1.0 H5' A:G6 2.6 35.8 1.0 O2' A:G5 2.9 31.6 1.0 O3' A:G5 3.2 29.6 1.0 O A:HOH212 3.3 36.4 0.3 C5' A:G6 3.5 29.8 1.0 H5'' A:G6 3.7 35.8 1.0 H4' A:G5 3.8 50.6 1.0 OP1 A:G6 3.9 30.7 1.0 C2' A:G5 3.9 28.2 1.0 C3' A:G5 4.0 34.8 1.0 P A:G6 4.0 31.4 1.0 O5' A:G6 4.2 29.1 1.0 H2' A:G5 4.4 33.8 1.0 C4' A:G5 4.4 42.2 1.0 H4' A:G6 4.5 35.4 1.0 C4' A:G6 4.6 29.5 1.0 H3' A:G5 4.9 41.8 1.0 O4' A:G6 4.9 30.5 1.0

Sodium binding site 3 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop 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 G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Methylguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:43.4 occ:1.00 HO3' A:CBV17 2.8 34.8 1.0 OP1 A:C18 2.9 33.0 1.0 O3' A:CBV17 3.3 29.0 1.0 NA A:NA108 3.7 47.2 1.0 P A:C18 3.8 28.1 1.0 H5'1 A:CBV17 3.8 32.2 1.0 O3 A:SO4104 4.0 0.6 0.3 O4 A:SO4104 4.1 0.3 0.3 O A:HOH202 4.1 31.4 0.3 H4' A:CBV17 4.3 33.7 1.0 S A:SO4104 4.5 0.8 0.3 C3' A:CBV17 4.5 27.7 1.0 HO2' A:CBV17 4.6 35.9 1.0 O1 A:SO4104 4.6 0.1 0.3 C5' A:CBV17 4.7 26.9 1.0 C4' A:CBV17 4.7 28.1 1.0 OP2 A:C18 4.7 33.0 1.0 H5'' A:C18 4.8 34.9 1.0 H5' A:C18 4.8 34.9 1.0 O5' A:C18 5.0 28.7 1.0

Sodium binding site 4 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop 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 G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Methylguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:47.2 occ:1.00 HO2' A:CBV17 2.1 35.9 1.0 HO3' A:CBV17 2.7 34.8 1.0 H5' A:C18 2.8 34.9 1.0 O2' A:CBV17 2.8 29.9 1.0 O3' A:CBV17 3.3 29.0 1.0 H4' A:CBV17 3.4 33.7 1.0 C5' A:C18 3.6 29.1 1.0 NA A:NA107 3.7 43.4 1.0 H5'' A:C18 3.7 34.9 1.0 C2' A:CBV17 3.9 28.0 1.0 C3' A:CBV17 3.9 27.7 1.0 OP1 A:C18 4.1 33.0 1.0 C4' A:CBV17 4.1 28.1 1.0 P A:C18 4.2 28.1 1.0 O5' A:C18 4.3 28.7 1.0 H2' A:CBV17 4.4 33.6 1.0 H4' A:C18 4.7 39.2 1.0 C4' A:C18 4.7 32.7 1.0 H3' A:CBV17 4.9 33.2 1.0 C1' A:CBV17 4.9 25.5 1.0 H5'1 A:CBV17 4.9 32.2 1.0 H1' A:CBV17 5.0 30.6 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