Sodium in PDB 8i3z: Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom

The structure of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom, PDB code: 8i3z was solved by X.Peng, D.M.J.Lilley, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.59 / 1.67
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.271, 81.271, 61.855, 90, 90, 120
R / Rfree (%)	16.8 / 18.6

The structure of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom (pdb code 8i3z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom, PDB code: 8i3z:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom


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 Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:57.1 occ:1.00 H8 A:A16 1.9 83.6 1.0 H2' A:A16 2.6 64.1 1.0 C8 A:A16 2.8 69.6 1.0 OP1 A:G15 2.8 35.5 1.0 OP1 A:A16 2.9 34.9 1.0 H5'' A:G15 3.4 41.0 1.0 O A:HOH209 3.5 48.5 1.0 C2' A:A16 3.5 53.4 1.0 N7 A:A16 3.5 76.4 1.0 HO2' A:A16 3.7 68.3 1.0 P A:G15 3.7 33.7 1.0 O5' A:A16 3.7 40.9 1.0 O2' A:A16 3.8 56.9 1.0 N9 A:A16 3.8 66.2 1.0 O5' A:G15 3.9 32.6 1.0 P A:A16 3.9 36.4 1.0 C5' A:G15 4.1 34.1 1.0 C1' A:A16 4.2 58.5 1.0 OP2 A:G15 4.2 31.8 1.0 H3' A:A16 4.6 60.3 1.0 H5' A:G15 4.6 41.0 1.0 C3' A:A16 4.6 50.2 1.0 C5 A:A16 4.8 78.2 1.0 H3' A:G15 4.8 37.0 1.0 O4' A:A16 4.8 54.9 1.0 OP2 A:A16 4.9 38.2 1.0 C4 A:A16 4.9 73.2 1.0 C5' A:A16 5.0 43.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom


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 Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:47.9 occ:1.00 N3 B:U40 3.0 32.9 1.0 O A:HOH205 3.0 44.6 1.0 O A:HOH201 3.1 39.9 1.0 H1' B:U39 3.4 37.7 1.0 H4' A:A3 3.5 42.3 1.0 O2 B:U40 3.7 42.0 1.0 O2' A:A3 3.7 35.1 1.0 O4' A:A3 3.7 33.5 1.0 C2 B:U40 3.8 36.4 1.0 O4 B:U40 3.8 33.0 1.0 C4 B:U40 3.9 33.0 1.0 HO2' A:A3 4.0 42.1 1.0 C4' A:A3 4.1 35.2 1.0 H1' A:A3 4.1 43.1 1.0 C1' B:U39 4.1 31.4 1.0 HO2' A:G2 4.2 43.2 1.0 O4' B:U39 4.2 36.9 1.0 C1' A:A3 4.4 35.9 1.0 C2' A:A3 4.6 33.4 1.0 O2 B:U39 4.6 37.6 1.0 N1 B:U39 4.6 35.1 1.0 O2' A:G2 4.7 36.0 1.0 C2 B:U39 4.8 37.3 1.0 H4' B:U39 4.8 42.6 1.0 C3' A:A3 4.8 34.0 1.0 O3' B:U39 5.0 43.2 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:63.1 occ:1.00 H5' B:G54 3.3 38.1 1.0 HO2' B:A53 3.5 37.1 1.0 H4' B:G54 3.6 32.4 1.0 O B:HOH257 3.8 39.2 1.0 O B:HOH211 3.9 42.9 1.0 C5' B:G54 4.0 31.8 1.0 H5'' B:G54 4.0 38.1 1.0 O B:HOH261 4.0 50.5 1.0 C4' B:G54 4.2 26.9 1.0 O2' B:A53 4.2 30.9 1.0 O4' B:G54 4.6 27.5 1.0 O B:HOH274 4.7 30.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Na105 b:63.6 occ:1.00 O B:HOH259 2.3 42.9 1.0 O B:HOH268 3.3 32.3 1.0 OP2 B:C35 3.4 35.8 1.0 O B:HOH236 3.6 50.0 1.0 H5 B:U36 3.6 41.1 1.0 H5 B:C35 4.2 38.8 1.0 O4 B:U36 4.4 35.8 1.0 C5 B:U36 4.4 34.4 1.0 P B:C35 4.6 37.6 1.0 C5 B:C35 4.7 32.5 1.0 O B:HOH255 4.8 43.4 1.0 H41 B:C37 4.8 35.2 1.0 C4 B:U36 4.8 36.7 1.0 H6 B:C35 4.9 38.3 1.0 O5' B:C35 4.9 36.9 1.0 OP2 B:U36 4.9 39.1 1.0

X.Peng, W.Liao, X.Lin, D.M.J.Lilley, L.Huang. Crystal Structures of the Nad+-II Riboswitch Reveal Two Distinct Ligand-Binding Pockets. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 36840714
DOI: 10.1093/NAR/GKAD102