Magnesium in PDB 2hom: Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Monophosphate

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Monophosphate, PDB code: 2hom 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 / 2.89
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	65.700, 65.700, 101.700, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 26.6

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

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Monophosphate (pdb code 2hom). 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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Monophosphate, PDB code: 2hom:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Monophosphate


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 Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg98 b:48.2 occ:1.00 O6 A:G78 2.2 75.0 1.0 O A:HOH96 2.3 40.0 1.0 O6 A:G60 2.5 70.1 1.0 O3 A:TPS97 2.5 79.7 1.0 O2 A:TPS97 2.8 82.0 1.0 C6 A:G78 3.0 76.1 1.0 N1 A:G78 3.0 75.0 1.0 P1 A:TPS97 3.1 82.5 1.0 C6 A:G60 3.6 71.2 1.0 O7 A:TPS97 3.7 79.4 1.0 O4 A:U59 3.9 73.4 1.0 N1 A:G60 3.9 70.1 1.0 N3 A:C77 4.0 85.6 1.0 N4 A:C77 4.3 86.7 1.0 C2 A:G78 4.3 75.8 1.0 C5 A:G78 4.4 77.5 1.0 O1 A:TPS97 4.5 85.7 1.0 C4 A:C77 4.6 86.5 1.0 C7 A:TPS97 4.7 73.9 1.0 N1 A:A61 4.8 70.1 1.0 N2 A:G78 4.8 75.4 1.0 C4 A:U59 4.8 77.6 1.0 C2 A:A61 4.8 70.7 1.0 C5 A:G60 4.9 72.5 1.0 C2 A:C77 4.9 85.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Monophosphate


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 Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg99 b:81.1 occ:1.00 O1 A:TPS97 2.9 85.7 1.0 O3 A:TPS97 3.4 79.7 1.0 N4 A:C77 3.4 86.7 1.0 P1 A:TPS97 3.7 82.5 1.0 N7 A:G76 4.2 87.8 1.0 C4 A:C77 4.3 86.5 1.0 N7 A:A75 4.4 89.2 1.0 O6 A:G76 4.6 91.8 1.0 N3 A:C77 4.7 85.6 1.0 O2 A:TPS97 4.8 82.0 1.0 N6 A:A75 4.8 91.0 1.0 O A:HOH96 4.8 40.0 1.0 C5 A:A75 4.9 90.1 1.0 O7 A:TPS97 4.9 79.4 1.0 OP2 A:A75 5.0 86.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Monophosphate


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:65.8 occ:1.00 O A:HOH92 2.4 29.3 1.0 O A:HOH94 2.7 44.1 1.0 O A:HOH93 2.9 48.4 1.0 N7 A:G40 3.5 58.7 1.0 C8 A:G40 4.3 57.4 1.0 OP2 A:U39 4.5 56.1 1.0 C5 A:G40 4.7 60.0 1.0 O6 A:G40 4.8 66.5 1.0 C5 A:U39 4.8 60.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Monophosphate


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:66.4 occ:1.00 O2' A:U62 2.5 85.5 1.0 O5' A:C63 2.8 74.6 1.0 O3' A:U62 3.0 78.3 1.0 OP1 A:C63 3.3 74.8 1.0 P A:C63 3.3 74.3 1.0 C2' A:U62 3.6 82.8 1.0 C3' A:U62 3.8 82.0 1.0 CA A:CA100 3.9 71.6 1.0 C5' A:C63 4.0 72.4 1.0 O3' A:C63 4.3 71.5 1.0 OP2 A:U64 4.4 73.4 1.0 C1' A:U62 4.6 84.0 1.0 P A:U64 4.7 73.7 1.0 OP1 A:U64 4.7 70.5 1.0 C4' A:C63 4.7 72.1 1.0 OP2 A:C63 4.8 74.3 1.0 C3' A:C63 4.8 71.9 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