Magnesium in PDB 2hoj: Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions, PDB code: 2hoj was solved by T.E.Edwards, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	64.700, 64.700, 101.900, 90.00, 90.00, 120.00
R / Rfree (%)	22.9 / 25.7

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions also contains other interesting chemical elements:

Manganese

(Mn)

12 atoms

The binding sites of Magnesium atom in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions (pdb code 2hoj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions, PDB code: 2hoj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg127 b:36.7 occ:1.00 OP2 A:C38 2.3 28.5 1.0 OP2 A:G37 2.9 32.4 1.0 O5' A:G37 3.0 30.6 1.0 P A:G37 3.4 35.5 1.0 C3' A:G37 3.6 28.6 1.0 P A:C38 3.6 28.0 1.0 C5 A:C38 3.8 24.1 1.0 C8 A:G37 3.9 34.5 1.0 OP1 A:G37 3.9 36.4 1.0 O3' A:G37 4.0 27.3 1.0 C5' A:G37 4.1 25.7 1.0 N7 A:G37 4.2 34.0 1.0 O5' A:C38 4.3 27.2 1.0 C4' A:G37 4.3 28.8 1.0 C6 A:C38 4.4 23.8 1.0 N9 A:G37 4.4 32.5 1.0 C2' A:G37 4.6 28.5 1.0 OP1 A:C38 4.9 29.0 1.0 O4' A:G37 4.9 29.4 1.0 C5 A:G37 4.9 33.4 1.0 O3' A:G36 4.9 35.4 1.0 C1' A:G37 4.9 29.5 1.0 C4 A:C38 5.0 25.6 1.0 C4 A:G37 5.0 31.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg128 b:35.0 occ:1.00 N3 A:G21 2.4 31.5 1.0 OP1 A:C73 2.6 42.7 1.0 O2' A:G21 2.6 36.5 1.0 C2' A:G21 2.8 35.0 1.0 O2' A:U71 3.0 36.5 1.0 O2 A:U71 3.2 39.7 1.0 C2 A:G21 3.3 29.9 1.0 N2 A:G21 3.3 27.0 1.0 C1' A:G21 3.4 35.1 1.0 C4 A:G21 3.5 30.4 1.0 O4' A:C22 3.5 32.7 1.0 C2' A:U71 3.8 38.2 1.0 N9 A:G21 3.8 33.4 1.0 P A:C73 3.9 39.2 1.0 N6 A:A43 4.0 25.4 1.0 C1' A:U71 4.0 37.9 1.0 N1 A:A43 4.2 21.6 1.0 C2 A:U71 4.3 39.1 1.0 C3' A:G21 4.3 34.6 1.0 C1' A:C22 4.3 28.7 1.0 C6 A:A43 4.3 23.8 1.0 OP2 A:C73 4.4 40.0 1.0 C4' A:C22 4.6 31.9 1.0 N1 A:G21 4.6 30.4 1.0 N1 A:C22 4.7 28.6 1.0 O4' A:G21 4.7 35.3 1.0 N1 A:U71 4.7 38.0 1.0 C6 A:C22 4.7 25.0 1.0 C3' A:G72 4.7 53.3 1.0 C5 A:G21 4.8 29.6 1.0 O5' A:C73 4.8 39.9 1.0 C5' A:C22 4.9 32.4 1.0 O3' A:G21 4.9 33.8 1.0 O3' A:G72 4.9 47.4 1.0

T.E.Edwards, A.R.Ferre-D'amare. Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive Rna-Small Molecule Recognition Structure V. 14 1459 2006.
ISSN: ISSN 0969-2126
PubMed: 16962976
DOI: 10.1016/J.STR.2006.07.008