Magnesium in PDB 8fb3: PREQ1-1 (Type-1) Riboswitch with Stacked Metabolites and A C10-G34 Base Pair in the Expression Platform

The structure of PREQ1-1 (Type-1) Riboswitch with Stacked Metabolites and A C10-G34 Base Pair in the Expression Platform, PDB code: 8fb3 was solved by J.E.Wedekind, G.M.Schroeder, J.L.Jenkins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.16 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.867, 67.612, 50.589, 90, 100.53, 90
R / Rfree (%)	22.5 / 26.5

The binding sites of Magnesium atom in the PREQ1-1 (Type-1) Riboswitch with Stacked Metabolites and A C10-G34 Base Pair in the Expression Platform (pdb code 8fb3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the PREQ1-1 (Type-1) Riboswitch with Stacked Metabolites and A C10-G34 Base Pair in the Expression Platform, PDB code: 8fb3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the PREQ1-1 (Type-1) Riboswitch with Stacked Metabolites and A C10-G34 Base Pair in the Expression Platform


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PREQ1-1 (Type-1) Riboswitch with Stacked Metabolites and A C10-G34 Base Pair in the Expression Platform within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:99.4 occ:1.00 OP1 B:A12 2.2 98.6 1.0 OP1 B:C13 2.3 105.8 1.0 OP1 A:U32 2.4 113.1 1.0 P A:U32 3.3 112.6 1.0 OP2 A:U32 3.5 98.6 1.0 P B:C13 3.5 101.5 1.0 P B:A12 3.6 89.0 1.0 O3' A:C31 3.8 103.5 1.0 OP2 B:C13 4.0 99.6 1.0 OP2 B:A12 4.2 88.3 1.0 O5' B:C13 4.2 106.2 1.0 O5' B:A12 4.3 86.2 1.0 O3' B:A11 4.6 98.0 1.0 C5' B:A12 4.6 84.7 1.0 O5' A:U32 4.7 109.3 1.0 O3' B:A12 4.8 98.1 1.0 C3' A:C31 5.0 104.4 1.0

Magnesium binding site 2 out of 3 in the PREQ1-1 (Type-1) Riboswitch with Stacked Metabolites and A C10-G34 Base Pair in the Expression Platform


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PREQ1-1 (Type-1) Riboswitch with Stacked Metabolites and A C10-G34 Base Pair in the Expression Platform within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:113.6 occ:1.00 OP1 A:A12 2.1 133.0 1.0 OP1 A:C13 2.6 126.8 1.0 O5' A:C13 3.1 144.6 1.0 C5' A:C13 3.4 153.0 1.0 P A:C13 3.5 129.3 1.0 P A:A12 3.5 122.9 1.0 O5' A:A12 4.2 114.4 1.0 O3' A:A11 4.3 120.4 1.0 O3' A:A12 4.3 129.1 1.0 C5' A:A12 4.4 118.7 1.0 OP2 A:A12 4.5 116.9 1.0 O4' A:C13 4.7 158.8 1.0 OP2 A:C13 4.7 125.0 1.0 C4' A:C13 4.7 155.5 1.0 C3' A:A12 4.9 119.1 1.0

Magnesium binding site 3 out of 3 in the PREQ1-1 (Type-1) Riboswitch with Stacked Metabolites and A C10-G34 Base Pair in the Expression Platform


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PREQ1-1 (Type-1) Riboswitch with Stacked Metabolites and A C10-G34 Base Pair in the Expression Platform within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg103 b:95.9 occ:1.00 OP1 C:C13 2.4 106.1 1.0 OP1 C:A12 2.9 104.9 1.0 P C:C13 3.8 106.9 1.0 P C:A12 4.3 102.3 1.0 C5' C:C13 4.4 111.1 1.0 O5' C:C13 4.5 106.3 1.0 OP2 C:C13 4.5 101.2 1.0 C5' C:A12 4.6 95.5 1.0 O4' C:C13 4.7 117.3 1.0 C6 C:C13 4.8 111.2 1.0 O5' C:A12 4.8 97.6 1.0 O3' C:A11 4.8 98.8 1.0 O3' C:A12 4.9 101.5 1.0

G.M.Schroeder, O.Akinyemi, J.Malik, C.M.Focht, E.M.Pritchett, C.D.Baker, J.P.Mcsally, J.L.Jenkins, D.H.Mathews, J.E.Wedekind. A Riboswitch Separated From Its Ribosome-Binding Site Still Regulates Translation. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 36762498
DOI: 10.1093/NAR/GKAD056