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

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions, PDB code: 2hok 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 / 3.20
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	66.300, 66.300, 101.600, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 29.1

The binding sites of Calcium atom in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions (pdb code 2hok). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions, PDB code: 2hok:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca94 b:40.8 occ:1.00 O1B A:TPP93 2.2 78.2 1.0 O2A A:TPP93 2.5 80.2 1.0 N4 A:C77 3.6 70.3 1.0 PB A:TPP93 3.8 75.8 1.0 PA A:TPP93 3.8 78.8 1.0 N7 A:A75 4.1 58.3 1.0 O1A A:TPP93 4.1 76.3 1.0 N7 A:G76 4.4 63.8 1.0 O3A A:TPP93 4.4 78.2 1.0 O3B A:TPP93 4.5 74.7 1.0 N6 A:A75 4.6 62.5 1.0 O2B A:TPP93 4.7 79.2 1.0 C5 A:A75 4.7 59.1 1.0 C4 A:C77 4.7 69.9 1.0 O A:HOH92 4.8 24.6 1.0 OP2 A:A75 4.8 52.6 1.0 C8 A:A75 4.8 58.4 1.0 C6 A:A75 4.9 59.4 1.0 O6 A:G76 5.0 69.0 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca95 b:47.1 occ:1.00 O6 A:G60 2.0 47.4 1.0 O6 A:G78 2.4 56.1 1.0 O A:HOH92 2.6 24.6 1.0 O2B A:TPP93 2.8 79.2 1.0 C6 A:G60 3.1 44.9 1.0 O3A A:TPP93 3.1 78.2 1.0 O4 A:U59 3.4 47.7 1.0 C6 A:G78 3.4 59.5 1.0 N1 A:G60 3.5 42.6 1.0 PB A:TPP93 3.5 75.8 1.0 N1 A:G78 3.6 60.1 1.0 N3 A:C77 4.2 70.0 1.0 O1A A:TPP93 4.3 76.3 1.0 N4 A:C77 4.3 70.3 1.0 O1B A:TPP93 4.3 78.2 1.0 C4 A:U59 4.3 48.3 1.0 PA A:TPP93 4.3 78.8 1.0 C5 A:G60 4.4 43.8 1.0 N1 A:A61 4.6 34.8 1.0 C5 A:G78 4.7 61.9 1.0 C4 A:C77 4.7 69.9 1.0 C2 A:G60 4.8 39.8 1.0 O3B A:TPP93 4.9 74.7 1.0 C2 A:A61 4.9 36.6 1.0 N6 A:A80 4.9 67.7 1.0 C2 A:G78 4.9 59.5 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca96 b:48.1 occ:1.00 OP2 A:U64 2.3 43.5 1.0 OP1 A:C63 2.6 49.4 1.0 P A:U64 3.6 43.0 1.0 P A:C63 4.1 49.3 1.0 OP1 A:U64 4.1 43.4 1.0 O3' A:C63 4.6 42.7 1.0 O3' A:U62 4.7 49.5 1.0 O5' A:U64 4.7 43.9 1.0 O5' A:C63 4.9 48.4 1.0 C3' A:C63 4.9 44.2 1.0 OP2 A:C63 5.0 48.1 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca97 b:63.8 occ:1.00 OP1 A:A69 2.3 53.8 1.0 P A:A69 3.7 52.8 1.0 O5' A:A69 4.1 52.0 1.0 O3' A:U68 4.5 51.9 1.0 C5' A:A69 4.7 50.6 1.0 OP2 A:A69 4.8 53.6 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca98 b:49.2 occ:1.00 OP2 A:A43 2.3 44.3 1.0 O6 A:G40 3.0 35.4 1.0 P A:A43 3.4 43.7 1.0 OP1 A:A43 3.7 44.2 1.0 C6 A:G40 3.8 34.6 1.0 N1 A:G40 3.8 34.2 1.0 O5' A:A43 4.1 47.0 1.0 OP1 A:A44 4.6 63.6 1.0 O3' A:G42 4.7 41.8 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca99 b:83.7 occ:1.00 OP1 A:A80 2.7 82.0 1.0 OP2 A:A80 3.0 82.5 1.0 OP2 A:G81 3.0 75.8 1.0 P A:A80 3.3 82.0 1.0 O5' A:A80 4.3 81.5 1.0 O6 A:G83 4.3 70.3 1.0 P A:G81 4.4 76.8 1.0 O3' A:U79 4.6 82.2 1.0 C3' A:A80 4.6 76.9 1.0 O3' A:A80 4.7 76.6 1.0 N7 A:G81 4.9 63.5 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca100 b:53.4 occ:1.00 OP2 A:U39 4.0 31.8 1.0 O6 A:G40 4.4 35.4 1.0 C5 A:U39 4.4 34.0 1.0 N7 A:G40 4.5 36.0 1.0 OP2 A:C38 4.9 35.5 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