Sodium in PDB 3suh: Crystal Structure of Thf Riboswitch, Bound with 5-Formyl-Thf

The structure of Crystal Structure of Thf Riboswitch, Bound with 5-Formyl-Thf, PDB code: 3suh was solved by L.Huang, A.Serganov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.65
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	126.597, 126.597, 149.164, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 24.6

The binding sites of Sodium atom in the Crystal Structure of Thf Riboswitch, Bound with 5-Formyl-Thf (pdb code 3suh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Thf Riboswitch, Bound with 5-Formyl-Thf, PDB code: 3suh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Thf Riboswitch, Bound with 5-Formyl-Thf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Thf Riboswitch, Bound with 5-Formyl-Thf within 5.0Å range: probe atom residue distance (Å) B Occ X:Na201 b:41.8 occ:1.00 O6 X:G76 2.5 26.4 1.0 O4 X:U78 2.6 31.3 1.0 O X:HOH107 2.7 27.6 1.0 C4 X:U78 3.5 28.5 1.0 C6 X:G76 3.5 27.9 1.0 N4 X:C75 3.7 26.4 1.0 O6 X:G20 3.8 36.2 1.0 N3 X:U78 3.9 27.0 1.0 N7 X:G76 4.1 26.0 1.0 N4 X:C21 4.1 25.3 1.0 C5 X:G76 4.1 27.2 1.0 C4 X:C75 4.6 27.6 1.0 C5 X:U78 4.6 25.8 1.0 N1 X:G76 4.7 27.7 1.0 C5 X:C75 4.8 24.4 1.0 C6 X:G20 5.0 35.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Thf Riboswitch, Bound with 5-Formyl-Thf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Thf Riboswitch, Bound with 5-Formyl-Thf within 5.0Å range: probe atom residue distance (Å) B Occ X:Na202 b:53.6 occ:1.00 O2' X:C21 3.9 28.8 1.0 O4' X:G27 4.0 32.2 1.0 C4' X:G27 4.3 27.9 1.0 O2' X:G27 4.3 30.4 1.0 O4' X:A79 4.4 34.5 1.0 C2 X:A26 4.5 31.4 1.0 N3 X:A26 4.5 32.2 1.0 N2 X:G20 4.5 36.1 1.0 C1' X:G27 4.5 29.5 1.0 O2' X:U78 4.6 25.0 1.0 O2 X:C21 4.8 26.2 1.0 C1' X:C21 4.8 24.5 1.0 C2' X:C21 4.9 24.9 1.0 C2' X:G27 5.0 28.3 1.0

L.Huang, S.Ishibe-Murakami, D.J.Patel, A.Serganov. Long-Range Pseudoknot Interactions Dictate the Regulatory Response in the Tetrahydrofolate Riboswitch. Proc.Natl.Acad.Sci.Usa V. 108 14801 2011.
ISSN: ISSN 0027-8424
PubMed: 21873197
DOI: 10.1073/PNAS.1111701108