Magnesium in PDB 8hb1: Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn

The structure of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn, PDB code: 8hb1 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)	35.64 / 2.23
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.314, 82.314, 63.248, 90, 90, 120
R / Rfree (%)	22.6 / 25

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

Bromine

(Br)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn (pdb code 8hb1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn, PDB code: 8hb1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:55.2 occ:1.00 H62 B:A48 2.0 62.3 1.0 N6 B:A48 2.8 51.8 1.0 OP2 A:G9 2.8 52.2 1.0 H3' A:U8 2.8 57.2 1.0 H2' A:U8 3.0 64.9 1.0 N7 B:A48 3.2 49.4 1.0 HC4 B:NMN102 3.2 62.9 1.0 H61 B:A48 3.3 62.3 1.0 HC5 B:NMN102 3.3 61.9 1.0 C6 A:U8 3.3 48.5 1.0 C4 B:NMN102 3.3 52.3 1.0 C5 B:NMN102 3.4 51.5 1.0 C5 A:U8 3.4 46.6 1.0 N1 A:U8 3.4 47.9 1.0 C4 A:U8 3.5 47.4 1.0 N3 A:U8 3.6 48.4 1.0 C2 A:U8 3.6 47.1 1.0 C3' A:U8 3.6 47.6 1.0 C2' A:U8 3.6 54.0 1.0 H6 A:U8 3.7 58.3 1.0 C6 B:A48 3.7 54.5 1.0 C5 B:A48 3.8 49.7 1.0 H5 A:U8 3.8 56.0 1.0 H41 A:C14 4.0 56.7 1.0 H3 A:U8 4.1 58.2 1.0 P A:G9 4.1 53.5 1.0 C3 B:NMN102 4.1 48.9 1.0 C1' A:U8 4.1 51.9 1.0 HN71 B:NMN102 4.1 62.0 1.0 MG A:MG103 4.2 62.0 1.0 O4 A:U8 4.2 49.7 1.0 C6 B:NMN102 4.3 47.0 1.0 O2 A:U8 4.3 50.1 1.0 H42 A:C14 4.3 56.7 1.0 O3' A:U8 4.3 47.9 1.0 C8 B:A48 4.4 52.8 1.0 O6 B:G51 4.5 48.5 1.0 N4 A:C14 4.5 47.1 1.0 O5' A:U8 4.6 50.3 1.0 H8 B:A48 4.7 63.4 1.0 N7 B:NMN102 4.7 51.5 1.0 H1 A:G15 4.7 56.7 1.0 O4' A:U8 4.8 45.4 1.0 C4' A:U8 4.8 49.0 1.0 HC6 B:NMN102 4.8 56.5 1.0 C2 B:NMN102 4.8 47.1 1.0 C7 B:NMN102 4.8 49.0 1.0 N1 B:NMN102 4.9 49.2 1.0 O2' A:U8 4.9 55.8 1.0 O5' A:G9 4.9 56.8 1.0 H1' A:U8 4.9 62.4 1.0 N1 B:A48 5.0 53.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:63.6 occ:1.00 H5' A:G11 2.2 58.7 1.0 H3' A:G11 2.7 62.0 1.0 H5 A:U12 2.7 56.3 1.0 OP2 A:U12 2.7 52.2 1.0 H6 A:U12 2.9 56.4 1.0 O2' A:C10 2.9 61.0 1.0 C5' A:G11 3.1 48.8 1.0 O3' A:C10 3.1 59.6 1.0 HO2' A:C10 3.2 73.4 1.0 C5 A:U12 3.4 46.9 1.0 C3' A:G11 3.4 51.5 1.0 C6 A:U12 3.5 46.9 1.0 O5' A:U12 3.5 51.7 1.0 H1' A:C10 3.5 64.6 1.0 O5' A:G11 3.6 59.7 1.0 P A:U12 3.6 51.3 1.0 C4' A:G11 3.7 51.2 1.0 H5'' A:G11 3.8 58.7 1.0 C2' A:C10 3.8 56.7 1.0 H4' A:G11 4.0 61.6 1.0 O3' A:G11 4.0 52.2 1.0 C3' A:C10 4.1 56.5 1.0 O2 A:C10 4.1 51.5 1.0 P A:G11 4.1 51.9 1.0 C1' A:C10 4.1 53.7 1.0 H5' A:U12 4.6 58.3 1.0 OP1 A:G9 4.6 51.0 1.0 H3' A:C10 4.6 67.9 1.0 C5' A:U12 4.6 48.5 1.0 C4 A:U12 4.7 42.5 1.0 H2' A:C10 4.7 68.2 1.0 H2' A:G11 4.7 67.2 1.0 C2' A:G11 4.7 55.9 1.0 N1 A:U12 4.8 46.8 1.0 OP1 A:G11 4.8 64.6 1.0 O4' A:U12 4.8 50.5 1.0 H21 B:G54 4.9 56.8 1.0 C2 A:C10 4.9 49.1 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:62.0 occ:1.00 H41 A:C13 2.4 57.5 1.0 HC5 B:NMN102 2.6 61.9 1.0 H5 A:C13 3.2 51.0 1.0 N4 A:C13 3.2 47.9 1.0 HC4 B:NMN102 3.4 62.9 1.0 H5 A:U12 3.5 56.3 1.0 C5 B:NMN102 3.5 51.5 1.0 O4 A:U12 3.6 48.7 1.0 OP2 A:G9 3.6 52.2 1.0 C5 A:U12 3.6 46.9 1.0 C4 A:U12 3.6 42.5 1.0 H42 A:C13 3.7 57.5 1.0 C4 B:NMN102 3.9 52.3 1.0 HO2' A:C10 3.9 73.4 1.0 C5 A:C13 3.9 42.4 1.0 C4 A:C13 4.0 42.6 1.0 OP1 A:G9 4.1 51.0 1.0 MG A:MG101 4.2 55.2 1.0 P A:G9 4.3 53.5 1.0 O2' A:C10 4.3 61.0 1.0 H41 A:C14 4.4 56.7 1.0 C6 A:U12 4.4 46.9 1.0 N3 A:U12 4.5 41.7 1.0 H3' A:U8 4.5 57.2 1.0 C6 B:NMN102 4.7 47.0 1.0 H6 A:U12 4.8 56.4 1.0 H3 A:U12 4.8 50.1 1.0 HC6 B:NMN102 4.9 56.5 1.0 H61 B:A53 4.9 60.6 1.0 N4 A:C14 5.0 47.1 1.0 O3' A:U8 5.0 47.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:63.1 occ:1.00 H22 B:G33 2.7 69.9 1.0 H1' B:A47 3.2 68.0 1.0 HO2' B:G33 3.3 84.1 1.0 N2 B:G33 3.5 58.1 1.0 N3 B:G33 3.6 60.5 1.0 O2' B:G33 3.8 70.0 1.0 H4' B:G34 3.8 72.3 1.0 C2 B:G33 4.1 58.3 1.0 C1' B:A47 4.1 56.5 1.0 H2' B:G33 4.1 75.2 1.0 H21 B:G33 4.1 69.9 1.0 O4' B:G34 4.1 63.2 1.0 O4' B:A47 4.2 54.7 1.0 HO2' B:G34 4.3 77.7 1.0 HO2' B:A47 4.4 71.0 1.0 C2' B:G33 4.5 62.5 1.0 C4' B:G34 4.5 60.2 1.0 H5' B:G34 4.5 72.1 1.0 H1' B:G33 4.5 74.7 1.0 HO2' B:C46 4.6 75.3 1.0 H1' B:G34 4.7 74.0 1.0 O2' B:A47 4.7 59.1 1.0 O2' B:C46 4.7 62.6 1.0 C4 B:G33 4.8 59.3 1.0 N9 B:A47 4.9 59.0 1.0 H4' B:A47 4.9 67.4 1.0 C1' B:G33 4.9 62.2 1.0 C1' B:G34 5.0 61.6 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