Barium in PDB 8hb8: Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn

The structure of Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn, PDB code: 8hb8 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)	27.26 / 2.30
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.362, 121.362, 109.055, 90, 90, 90
R / Rfree (%)	22.7 / 25.3

The binding sites of Barium atom in the Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn (pdb code 8hb8). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 7 binding sites of Barium where determined in the Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn, PDB code: 8hb8:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7;

Barium binding site 1 out of 7 in the Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba103 b:198.9 occ:1.00 OP2 A:U7 2.6 85.4 1.0 O3' A:G6 3.2 74.1 1.0 P A:U7 3.5 69.0 1.0 O6 A:G15 3.5 62.7 1.0 N7 A:G15 3.5 67.0 1.0 O2' A:G6 3.6 76.9 1.0 HO2' A:G6 3.7 92.2 1.0 H5 A:C14 3.7 75.5 1.0 OP2 A:U8 3.8 82.3 1.0 O5' A:U7 4.0 78.9 1.0 C5 A:C14 4.1 62.9 1.0 H1' A:G6 4.1 89.0 1.0 C6 A:G15 4.2 69.3 1.0 C5 A:G15 4.2 74.3 1.0 H6 A:C14 4.2 84.6 1.0 H5'' A:C14 4.3 94.4 1.0 C3' A:G6 4.3 80.0 1.0 C6 A:C14 4.4 70.5 1.0 C2' A:G6 4.4 78.4 1.0 C8 A:G15 4.6 65.5 1.0 OP2 A:C14 4.7 64.2 1.0 H3' A:G6 4.8 96.0 1.0 C1' A:G6 4.8 74.2 1.0 H8 A:G15 4.8 78.6 1.0 OP1 A:U7 4.8 103.2 1.0 H3' A:C14 4.8 79.4 1.0 H3' A:U7 4.9 83.6 1.0 C4 A:C14 5.0 73.2 1.0

Barium binding site 2 out of 7 in the Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba104 b:190.5 occ:1.00 O2P A:NMN101 3.7 85.3 1.0 O6 A:G4 4.2 95.6 1.0 O6 A:G3 4.3 93.2 1.0 N7 A:G3 4.4 97.9 1.0 N7 A:G4 4.9 91.8 1.0 H41 A:C5 4.9 97.5 1.0 H42 A:C35 4.9 109.7 1.0 C6 A:G3 4.9 91.1 1.0 C5 A:G3 5.0 97.6 1.0

Barium binding site 3 out of 7 in the Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba105 b:186.5 occ:1.00 OP1 A:A47 3.8 75.5 1.0 P A:A47 4.9 68.5 1.0 N7 A:G11 4.9 62.4 1.0

Barium binding site 4 out of 7 in the Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba106 b:181.1 occ:0.69 O1P A:NMN102 2.7 83.8 1.0 HO2' A:A48 3.3 70.0 1.0 H5'' A:A49 3.7 121.1 1.0 O2' A:A48 3.8 58.3 1.0 H1' A:A48 4.0 78.9 1.0 O3' A:A48 4.1 81.7 1.0 P A:NMN102 4.2 77.6 1.0 H5' A:A49 4.3 121.1 1.0 C5' A:A49 4.5 100.9 1.0 OP2 A:A49 4.5 88.5 1.0 O7 A:NMN102 4.6 67.8 1.0 H5R1 A:NMN102 4.7 76.4 1.0 C2' A:A48 4.7 63.2 1.0 C1' A:A48 4.8 65.7 1.0 O3P A:NMN102 4.9 104.6 1.0 P A:A49 4.9 79.8 1.0

Barium binding site 5 out of 7 in the Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba107 b:201.8 occ:1.00 OP2 A:A49 4.1 88.5 1.0 OP2 A:C10 4.5 57.9 1.0 P A:A49 5.0 79.8 1.0

Barium binding site 6 out of 7 in the Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba108 b:211.2 occ:1.00 O4 A:U20 4.0 77.8 1.0 OP2 A:A18 4.1 75.8 1.0 N7 A:G19 4.4 84.1 1.0 H61 A:A29 4.4 98.6 1.0 O6 A:G19 4.6 74.9 1.0 H62 A:A29 4.8 98.6 1.0 OP2 A:G19 4.9 83.2 1.0 N6 A:A29 5.0 82.2 1.0

Barium binding site 7 out of 7 in the Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of Nad-II Riboswitch (Single Strand) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba109 b:202.5 occ:1.00 O3' A:U7 4.9 66.9 1.0 OP1 A:U8 4.9 89.5 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