Calcium in PDB 3fu2: Cocrystal Structure of A Class-I PREQ1 Riboswitch

The structure of Cocrystal Structure of A Class-I PREQ1 Riboswitch, PDB code: 3fu2 was solved by D.J.Klein, 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 / 2.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.208, 78.208, 85.220, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 26.7

The binding sites of Calcium atom in the Cocrystal Structure of A Class-I PREQ1 Riboswitch (pdb code 3fu2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Cocrystal Structure of A Class-I PREQ1 Riboswitch, PDB code: 3fu2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Cocrystal Structure of A Class-I PREQ1 Riboswitch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cocrystal Structure of A Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:43.4 occ:1.00 O A:HOH812 2.0 21.2 1.0 OP2 A:U9 2.3 41.0 1.0 O A:HOH810 2.4 30.5 1.0 OP2 A:U7 2.4 37.6 1.0 O A:HOH811 2.4 30.0 1.0 P A:U9 3.7 41.2 1.0 P A:U7 3.8 37.8 1.0 O5' A:U9 4.2 40.0 1.0 O5' A:U7 4.3 35.4 1.0 OP1 A:U9 4.3 40.5 1.0 C5 A:U9 4.6 35.7 1.0 OP2 A:A10 4.6 34.8 1.0 O5' A:U6 4.7 38.2 1.0 OP1 A:U7 4.7 38.3 1.0 N7 A:A10 4.7 36.3 1.0 O3' A:U6 4.8 38.1 1.0 C3' A:U6 4.8 37.0 1.0 C5 A:U7 4.8 45.3 1.0 OP2 A:U6 4.8 40.4 1.0 O3' A:C8 4.8 39.8 1.0 C6 A:U9 4.9 35.5 1.0

Calcium binding site 2 out of 9 in the Cocrystal Structure of A Class-I PREQ1 Riboswitch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cocrystal Structure of A Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:44.6 occ:1.00 O B:HOH801 2.0 29.5 1.0 O B:HOH802 2.1 26.7 1.0 OP2 B:C21 2.6 31.4 1.0 OP2 A:C21 2.6 36.5 1.0 O A:HOH803 3.6 21.7 1.0 P A:C21 3.8 36.3 1.0 P B:C21 3.9 32.2 1.0 O B:HOH804 4.1 25.6 1.0 OP1 A:C21 4.2 36.2 1.0 OP1 B:C21 4.4 32.6 1.0 C5 A:C21 4.4 34.1 1.0 O3' A:U20 4.5 36.6 1.0 O3' B:U20 4.5 34.2 1.0 C3' A:U20 4.6 34.1 1.0 C5 B:C21 4.6 32.9 1.0 C3' B:U20 4.7 34.2 1.0 O5' A:U20 4.7 37.2 1.0 C6 A:C21 4.8 33.2 1.0 OP2 B:U20 4.8 39.6 1.0 O5' B:U20 4.8 38.6 1.0 OP2 A:U20 4.9 39.3 1.0 OP1 B:U20 4.9 40.8 1.0

Calcium binding site 3 out of 9 in the Cocrystal Structure of A Class-I PREQ1 Riboswitch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cocrystal Structure of A Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca906 b:42.5 occ:0.50 O2 A:C8 4.0 37.8 1.0 C2 A:A34 4.5 48.5 1.0 N3 A:C8 4.6 39.9 1.0 N3 A:A34 4.6 48.7 1.0 C2 A:C8 4.7 38.8 1.0 O2 A:U9 4.9 40.0 1.0

Calcium binding site 4 out of 9 in the Cocrystal Structure of A Class-I PREQ1 Riboswitch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cocrystal Structure of A Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca907 b:67.7 occ:1.00 N7 A:A34 3.7 48.5 1.0 OP2 A:A33 3.8 51.5 1.0 N6 A:A34 4.0 50.1 1.0 C8 A:A33 4.4 49.0 1.0 N7 A:A33 4.4 48.1 1.0 O5' A:A33 4.6 51.7 1.0 C5 A:A34 4.6 49.3 1.0 C8 A:A34 4.7 48.9 1.0 C6 A:A34 4.8 48.8 1.0 P A:A33 4.8 53.5 1.0 OP2 A:A34 4.8 54.9 1.0

Calcium binding site 5 out of 9 in the Cocrystal Structure of A Class-I PREQ1 Riboswitch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cocrystal Structure of A Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca908 b:1.0 occ:1.00 OP1 B:U22 4.4 35.6 1.0 O6 A:G2 4.5 45.1 1.0 N7 A:A1 4.8 41.8 1.0

Calcium binding site 6 out of 9 in the Cocrystal Structure of A Class-I PREQ1 Riboswitch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cocrystal Structure of A Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:49.8 occ:1.00 OP2 B:U9 2.2 50.6 1.0 OP2 B:U7 2.3 55.0 1.0 O B:HOH805 2.4 32.2 1.0 O B:HOH806 2.8 30.5 1.0 P B:U9 3.6 50.6 1.0 P B:U7 3.7 54.9 1.0 O5' B:U9 4.2 47.4 1.0 O5' B:U7 4.2 54.1 1.0 C5 B:U9 4.3 33.4 1.0 OP1 B:U7 4.4 55.7 1.0 OP1 B:U9 4.5 48.5 1.0 N7 B:A10 4.6 33.1 1.0 O3' B:C8 4.6 51.0 1.0 C5 B:U7 4.7 58.5 1.0 OP2 B:A10 4.7 33.2 1.0 C6 B:U9 4.7 33.5 1.0 O3' B:U6 4.8 52.8 1.0 O5' B:U6 4.9 46.2 1.0 C3' B:C8 4.9 50.7 1.0 C3' B:U6 4.9 49.2 1.0 OP2 B:U6 5.0 47.1 1.0 C6 B:U7 5.0 58.7 1.0

Calcium binding site 7 out of 9 in the Cocrystal Structure of A Class-I PREQ1 Riboswitch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cocrystal Structure of A Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca909 b:87.6 occ:1.00 O6 B:G2 3.9 39.4 1.0 N6 B:A1 4.3 43.9 1.0 OP1 A:U22 4.4 35.0 1.0 N7 B:A1 4.4 46.2 1.0 OP2 A:U22 4.9 30.1 1.0 C6 B:G2 4.9 41.0 1.0 N7 B:G2 4.9 40.5 1.0 C5 B:A1 5.0 45.3 1.0 C6 B:A1 5.0 44.5 1.0

Calcium binding site 8 out of 9 in the Cocrystal Structure of A Class-I PREQ1 Riboswitch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cocrystal Structure of A Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca904 b:43.3 occ:1.00 OP2 C:U7 2.4 53.1 1.0 OP2 C:U9 2.6 46.9 1.0 P C:U7 3.8 52.4 1.0 P C:U9 4.0 48.5 1.0 O5' C:U7 4.2 51.5 1.0 C5 C:U7 4.4 62.5 1.0 O5' C:U9 4.5 46.6 1.0 OP2 C:A10 4.6 43.1 1.0 OP1 C:U7 4.6 50.0 1.0 N7 C:A10 4.7 35.0 1.0 OP2 C:U6 4.7 45.2 1.0 OP1 C:U9 4.7 46.6 1.0 C6 C:U7 4.8 62.3 1.0 O5' C:U6 4.8 44.7 1.0 O3' C:U6 4.8 49.5 1.0 C3' C:U6 4.9 48.2 1.0 C5 C:U9 4.9 38.7 1.0

Calcium binding site 9 out of 9 in the Cocrystal Structure of A Class-I PREQ1 Riboswitch


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cocrystal Structure of A Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca905 b:62.1 occ:1.00 O2 C:C8 2.5 50.2 1.0 C2 C:C8 3.6 47.6 1.0 N3 C:C8 4.2 48.0 1.0 N1 C:C8 4.7 45.8 1.0 C1' C:C8 4.9 45.8 1.0

D.J.Klein, T.E.Edwards, A.R.Ferre-D'amare. Cocrystal Structure of A Class I PREQ1 Riboswitch Reveals A Pseudoknot Recognizing An Essential Hypermodified Nucleobase Nat.Struct.Mol.Biol. V. 16 343 2009.
ISSN: ISSN 1545-9993
PubMed: 19234468
DOI: 10.1038/NSMB.1563