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Sodium in PDB 6hc5: The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Audouine

Protein crystallography data

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Audouine, PDB code: 6hc5 was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.91 / 1.41
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 55.826, 55.826, 133.363, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 19.9

Other elements in 6hc5:

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Audouine also contains other interesting chemical elements:

Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Audouine (pdb code 6hc5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Audouine, PDB code: 6hc5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6hc5

Go back to Sodium Binding Sites List in 6hc5
Sodium binding site 1 out of 3 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Audouine


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 P2 Stem-Loop with Audouine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na102

b:67.8
occ:1.00
N7 A:G2 3.3 34.2 1.0
N7 A:G1 4.0 31.9 1.0
C8 A:G2 4.1 34.2 1.0
OP2 A:G2 4.1 41.9 1.0
C8 A:G1 4.4 31.7 1.0
C5 A:G2 4.5 33.2 1.0
C5 A:G1 4.5 31.6 1.0
O6 A:G2 4.6 32.9 1.0
C6 A:G1 4.9 32.6 1.0
O6 A:G1 4.9 32.7 1.0
C6 A:G2 5.0 32.4 1.0
O5' A:G1 5.0 39.5 1.0

Sodium binding site 2 out of 3 in 6hc5

Go back to Sodium Binding Sites List in 6hc5
Sodium binding site 2 out of 3 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Audouine


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 P2 Stem-Loop with Audouine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na103

b:84.4
occ:1.00
N7 A:G5 2.8 36.7 1.0
O A:HOH230 3.0 61.5 1.0
O A:HOH216 3.1 50.1 1.0
C8 A:G5 3.8 35.9 1.0
C5 A:G5 3.9 34.0 1.0
O6 A:G5 3.9 37.9 1.0
N7 A:G4 4.0 28.8 1.0
C6 A:G5 4.3 36.0 1.0
O6 A:G4 4.4 34.2 1.0
C5 A:G4 4.5 29.9 1.0
C6 A:G4 4.6 35.3 1.0
C8 A:G4 4.8 32.5 1.0
N9 A:G5 5.0 34.2 1.0

Sodium binding site 3 out of 3 in 6hc5

Go back to Sodium Binding Sites List in 6hc5
Sodium binding site 3 out of 3 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Audouine


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 P2 Stem-Loop with Audouine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na104

b:64.7
occ:1.00
N4 A:C15 2.9 42.8 1.0
N4 A:C14 3.6 36.7 1.0
C4 A:C15 3.8 38.5 1.0
C5 A:C15 3.8 37.7 1.0
C5 A:C14 3.9 34.5 1.0
C4 A:C14 3.9 35.9 1.0
O A:HOH229 4.0 55.9 1.0
N6 A:A16 4.4 30.9 1.0
O A:HOH205 4.5 67.3 1.0
O A:HOH222 4.7 46.0 1.0
O A:HOH201 4.8 79.8 1.0
C6 A:C14 4.9 34.5 1.0
N3 A:C14 4.9 36.5 1.0

Reference:

L.Huang, J.Wang, T.J.Wilson, D.M.J.Lilley. Structure-Guided Design of A High-Affinity Ligand For A Riboswitch. Rna V. 25 423 2019.
ISSN: ESSN 1469-9001
PubMed: 30609994
DOI: 10.1261/RNA.069567.118
Page generated: Tue Dec 15 12:20:05 2020

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