Manganese 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:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese 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 Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions, PDB code: 2hoj:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 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 Manganese with other atoms in the Mn 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:Mn115 b:36.0 occ:1.00 O1B A:TPP114 1.9 65.8 1.0 O A:HOH113 1.9 79.0 1.0 O2A A:TPP114 2.1 67.4 1.0 O A:HOH112 2.2 21.3 1.0 O A:HOH109 2.4 26.2 1.0 O A:HOH104 2.5 28.0 1.0 PB A:TPP114 2.9 58.8 1.0 O3B A:TPP114 3.0 59.0 1.0 PA A:TPP114 3.4 63.0 1.0 O1A A:TPP114 3.7 67.8 1.0 O3A A:TPP114 3.8 65.3 1.0 N4 A:C77 4.2 51.2 1.0 O2B A:TPP114 4.2 59.0 1.0 N7 A:A75 4.3 46.9 1.0 O7 A:TPP114 4.7 65.9 1.0 N7 A:G76 4.8 47.2 1.0 N6 A:A75 4.8 48.9 1.0 OP2 A:A75 4.9 43.9 1.0 O A:HOH101 4.9 11.5 1.0 O6 A:G76 4.9 44.5 1.0 C5 A:A75 5.0 47.3 1.0

Manganese binding site 2 out of 12 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 Manganese with other atoms in the Mn 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:Mn116 b:31.5 occ:1.00 O A:HOH103 2.0 29.5 1.0 O A:HOH105 2.1 14.7 1.0 O6 A:G60 2.2 34.7 1.0 O A:HOH101 2.2 11.5 1.0 O2B A:TPP114 2.3 59.0 1.0 O6 A:G78 2.5 31.9 1.0 C6 A:G60 3.3 34.2 1.0 C6 A:G78 3.4 35.8 1.0 PB A:TPP114 3.4 58.8 1.0 O4 A:U59 3.6 33.9 1.0 N1 A:G78 3.7 32.1 1.0 N1 A:G60 3.7 33.5 1.0 O1B A:TPP114 3.8 65.8 1.0 O3A A:TPP114 3.8 65.3 1.0 N1 A:A61 4.0 37.7 1.0 N3 A:C77 4.3 45.9 1.0 C2 A:A61 4.3 34.8 1.0 C4 A:U59 4.4 39.8 1.0 O A:HOH109 4.5 26.2 1.0 C5 A:G60 4.5 36.0 1.0 O1A A:TPP114 4.7 67.8 1.0 O3B A:TPP114 4.7 59.0 1.0 C5 A:G78 4.8 39.3 1.0 N4 A:C77 4.8 51.2 1.0 PA A:TPP114 4.9 63.0 1.0 O2 A:C77 5.0 47.5 1.0 C5 A:U59 5.0 37.9 1.0 C2 A:G78 5.0 33.4 1.0

Manganese binding site 3 out of 12 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 Manganese with other atoms in the Mn binding site number 3 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:Mn117 b:35.6 occ:1.00 OP1 A:C63 1.9 33.7 1.0 O A:HOH107 2.1 50.9 1.0 OP2 A:U64 2.2 34.9 1.0 P A:C63 3.4 32.4 1.0 P A:U64 3.5 29.6 1.0 O3' A:C63 4.1 31.6 1.0 O3' A:U62 4.1 33.6 1.0 O5' A:C63 4.2 35.5 1.0 OP1 A:U64 4.2 29.2 1.0 OP2 A:C63 4.3 33.2 1.0 C3' A:C63 4.5 32.9 1.0 O5' A:U64 4.6 31.4 1.0

Manganese binding site 4 out of 12 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 Manganese with other atoms in the Mn binding site number 4 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:Mn118 b:43.0 occ:1.00 N7 A:A41 2.3 27.7 1.0 O A:HOH96 2.5 19.9 1.0 C8 A:A41 3.2 26.4 1.0 C5 A:A41 3.4 24.5 1.0 N6 A:A41 3.7 22.5 1.0 C6 A:A41 4.0 23.4 1.0 O2' A:G40 4.2 27.6 1.0 O6 A:G42 4.3 29.3 1.0 N9 A:A41 4.5 28.8 1.0 C4 A:A41 4.6 27.8 1.0 C6 A:G42 5.0 28.8 1.0

Manganese binding site 5 out of 12 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 Manganese with other atoms in the Mn binding site number 5 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:Mn119 b:49.8 occ:1.00 O A:HOH111 1.8 39.1 1.0 N7 A:G40 2.4 32.1 1.0 O A:HOH93 2.8 26.8 1.0 C8 A:G40 3.2 32.9 1.0 O A:HOH94 3.3 28.2 1.0 C5 A:G40 3.6 29.9 1.0 O6 A:G40 4.0 27.3 1.0 OP2 A:G40 4.2 35.2 1.0 C6 A:G40 4.2 29.1 1.0 N9 A:G40 4.5 30.8 1.0 OP2 A:U39 4.6 25.7 1.0 OP2 A:G42 4.7 30.4 1.0 C4 A:G40 4.7 28.5 1.0 C5 A:U39 4.7 29.9 1.0

Manganese binding site 6 out of 12 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 Manganese with other atoms in the Mn binding site number 6 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:Mn120 b:83.7 occ:1.00 OP2 A:A80 3.0 71.6 1.0 N7 A:G81 3.5 50.7 1.0 OP2 A:G81 4.1 63.9 1.0 P A:A80 4.2 72.3 1.0 N7 A:G82 4.2 44.3 1.0 O6 A:G81 4.3 48.1 1.0 C8 A:G81 4.3 52.9 1.0 OP1 A:A80 4.4 71.5 1.0 O6 A:G83 4.4 52.8 1.0 C5 A:G81 4.4 51.4 1.0 C6 A:G81 4.7 50.6 1.0 O6 A:G82 4.7 53.5 1.0 N7 A:A80 4.9 60.0 1.0 O3' A:U79 5.0 70.8 1.0

Manganese binding site 7 out of 12 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 Manganese with other atoms in the Mn binding site number 7 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:Mn121 b:92.3 occ:1.00 N7 A:G36 2.3 40.0 1.0 C8 A:G36 3.1 40.5 1.0 O A:HOH97 3.4 35.4 1.0 C5 A:G36 3.5 38.0 1.0 O6 A:G36 3.9 41.7 1.0 C6 A:G36 4.1 38.9 1.0 OP2 A:G36 4.1 50.7 1.0 OP2 A:A35 4.2 79.2 1.0 N9 A:G36 4.4 38.2 1.0 C4 A:G36 4.5 36.8 1.0 N7 A:A35 4.6 54.6 1.0 C8 A:A35 4.7 57.1 1.0 O5' A:A35 4.9 74.7 1.0 OP2 A:A34 4.9 85.3 1.0 O5' A:G36 4.9 48.9 1.0

Manganese binding site 8 out of 12 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 Manganese with other atoms in the Mn binding site number 8 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:Mn122 b:1.0 occ:1.00 OP1 A:A69 2.2 45.0 1.0 P A:A69 3.5 39.9 1.0 O5' A:A69 4.0 41.2 1.0 C5' A:A69 4.1 39.7 1.0 OP2 A:A69 4.2 44.0 1.0 O3' A:U68 4.6 42.5 1.0 O4' A:A69 4.7 38.9 1.0 C8 A:A69 4.9 38.1 1.0

Manganese binding site 9 out of 12 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 Manganese with other atoms in the Mn binding site number 9 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:Mn123 b:87.4 occ:1.00 N7 A:G66 3.7 42.0 1.0 O6 A:G66 3.9 49.2 1.0 N6 A:A67 4.2 43.6 1.0 C5 A:G66 4.5 46.9 1.0 N7 A:A67 4.5 49.4 1.0 C6 A:G66 4.6 46.5 1.0 C8 A:G66 4.8 45.7 1.0 N7 A:G65 5.0 49.9 1.0

Manganese binding site 10 out of 12 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 Manganese with other atoms in the Mn binding site number 10 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:Mn124 b:75.2 occ:1.00 OP2 A:A2391 2.3 41.7 1.0 P A:A2391 3.7 38.3 1.0 O3' A:C90 4.3 37.0 1.0 OP1 A:A2391 4.6 40.1 1.0 O5' A:A2391 4.7 41.1 1.0 C3' A:A2391 4.7 52.8 1.0 C2' A:A2391 4.8 54.1 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