Calcium in PDB 2hoo: Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine, PDB code: 2hoo 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 / 3.00
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	61.400, 61.400, 102.900, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 27.5

The binding sites of Calcium atom in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine (pdb code 2hoo). 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 Benfotiamine, PDB code: 2hoo:
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 Benfotiamine


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 Benfotiamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca96 b:70.9 occ:1.00 O6 A:G78 2.0 65.4 1.0 O3 A:BFT95 2.3 99.3 1.0 O6 A:G60 2.5 82.9 1.0 O A:HOH93 2.7 31.3 1.0 C6 A:G78 3.0 71.8 1.0 O4 A:U59 3.2 64.5 1.0 N1 A:G78 3.4 72.8 1.0 C6 A:G60 3.4 80.1 1.0 P1 A:BFT95 3.4 89.7 1.0 N1 A:G60 3.6 77.6 1.0 O1 A:BFT95 3.8 90.0 1.0 O2 A:BFT95 4.0 92.6 1.0 N1 A:G72 4.0 0.0 1.0 N2 A:G72 4.1 0.0 1.0 C4 A:U59 4.2 67.9 1.0 C5 A:G78 4.3 77.7 1.0 C2 A:G72 4.4 0.0 1.0 N1 A:A61 4.6 90.1 1.0 C2 A:A61 4.6 88.7 1.0 O7 A:BFT95 4.7 97.5 1.0 N3 A:C77 4.7 88.3 1.0 C2 A:G78 4.7 75.7 1.0 C5 A:G60 4.7 81.4 1.0 C6 A:G72 4.8 0.4 1.0 C5 A:U59 4.9 68.9 1.0 N4 A:C77 4.9 83.8 1.0 C2 A:G60 4.9 75.3 1.0 O6 A:G72 5.0 0.0 1.0 N7 A:G78 5.0 75.7 1.0

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


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 Benfotiamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca97 b:0.9 occ:1.00 N4 A:C77 3.2 83.8 1.0 N2 A:G72 3.2 0.0 1.0 O A:HOH92 3.3 42.5 1.0 O1 A:BFT95 3.4 90.0 1.0 N7 A:G76 3.6 0.6 1.0 O6 A:G76 3.8 0.8 1.0 O2 A:BFT95 4.1 92.6 1.0 N7 A:A75 4.1 93.3 1.0 C2 A:G72 4.2 0.0 1.0 C4 A:C77 4.2 86.1 1.0 N3 A:G72 4.2 0.2 1.0 P1 A:BFT95 4.3 89.7 1.0 C5 A:G76 4.4 0.1 1.0 C6 A:G76 4.4 0.4 1.0 OP2 A:A75 4.6 92.7 1.0 N3 A:C77 4.7 88.3 1.0 C8 A:G76 4.7 0.5 1.0 N6 A:A75 4.7 88.4 1.0 C5 A:A75 4.8 93.0 1.0 C8 A:A75 4.9 96.4 1.0

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


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 Benfotiamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca98 b:80.8 occ:1.00 OP1 A:A80 2.9 0.1 1.0 OP2 A:G81 3.2 88.4 1.0 N7 A:G81 3.8 59.4 1.0 O5' A:A80 3.9 0.6 1.0 O6 A:G83 4.0 66.1 1.0 P A:A80 4.1 0.4 1.0 N7 A:G82 4.1 41.6 1.0 C8 A:G81 4.3 67.7 1.0 OP2 A:U54 4.3 0.4 1.0 P A:G81 4.5 85.7 1.0 C5 A:G81 4.6 64.4 1.0 O5' A:G81 4.7 81.6 1.0 C6 A:G83 4.9 61.4 1.0 O6 A:G82 4.9 57.4 1.0 C8 A:G82 4.9 44.1 1.0 OP2 A:G82 4.9 73.5 1.0 O6 A:G81 5.0 68.4 1.0 C3' A:A80 5.0 84.3 1.0

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


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 Benfotiamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca99 b:0.0 occ:1.00 O6 A:G40 3.6 65.1 1.0 N7 A:G40 4.2 57.7 1.0 C6 A:G40 4.5 63.0 1.0 C5 A:G40 4.7 57.5 1.0 OP2 A:U39 4.8 62.0 1.0

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


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 Benfotiamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca100 b:0.6 occ:1.00 O2' A:U20 2.8 76.2 1.0 C2 A:A44 3.2 99.7 1.0 C2' A:U20 3.6 72.1 1.0 N1 A:A44 3.7 0.6 1.0 O3' A:U20 3.7 77.0 1.0 OP2 A:A44 3.9 92.9 1.0 OP2 A:G21 3.9 78.5 1.0 OP1 A:G21 4.0 76.8 1.0 P A:G21 4.0 78.7 1.0 C3' A:U20 4.1 72.1 1.0 N3 A:A44 4.1 98.2 1.0 O3' A:A43 4.2 85.1 1.0 O2' A:A43 4.3 78.9 1.0 P A:A44 4.7 91.4 1.0 C6 A:A44 4.9 1.0 1.0 C1' A:U20 5.0 69.6 1.0

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


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 Benfotiamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:97.6 occ:1.00 OP2 A:G36 2.6 0.4 1.0 OP2 A:A35 3.0 0.0 1.0 O5' A:A35 3.2 0.5 1.0 OP2 A:A34 3.4 0.0 1.0 N7 A:G36 3.5 80.6 1.0 P A:A35 3.7 0.1 1.0 C8 A:G36 3.8 79.7 1.0 C8 A:A35 3.9 0.8 1.0 P A:G36 4.0 0.6 1.0 C3' A:A35 4.0 0.4 1.0 N7 A:A35 4.1 0.5 1.0 C5' A:A35 4.5 0.6 1.0 OP1 A:A35 4.5 0.5 1.0 P A:A34 4.5 0.0 1.0 O3' A:A35 4.5 0.9 1.0 N9 A:A35 4.6 0.3 1.0 O5' A:G36 4.6 0.1 1.0 C4' A:A35 4.8 0.8 1.0 C5 A:G36 4.8 77.2 1.0 O5' A:A34 4.8 0.0 1.0 C5 A:A35 4.8 98.7 1.0 OP1 A:A34 4.9 0.9 1.0 C2' A:A35 5.0 0.4 1.0 O3' A:A34 5.0 0.1 1.0

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


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 Benfotiamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:0.9 occ:1.00 OP1 A:C55 2.7 0.9 1.0 P A:C55 3.7 0.3 1.0 O5' A:C55 3.7 0.5 1.0 OP2 A:C55 4.3 0.6 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