Calcium in PDB 3k1v: Cocrystal Structure of A Mutant Class-I PREQ1 Riboswitch

The structure of Cocrystal Structure of A Mutant Class-I PREQ1 Riboswitch, PDB code: 3k1v 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 / 2.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	76.810, 76.810, 85.900, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 26.9

The binding sites of Calcium atom in the Cocrystal Structure of A Mutant Class-I PREQ1 Riboswitch (pdb code 3k1v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cocrystal Structure of A Mutant Class-I PREQ1 Riboswitch, PDB code: 3k1v:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cocrystal Structure of A Mutant 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 Mutant Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:25.7 occ:1.00 OP2 A:C8 2.3 34.1 1.0 O A:HOH108 2.6 36.5 1.0 O A:HOH109 2.6 16.6 1.0 O A:HOH155 3.0 42.3 1.0 P A:C8 3.7 30.6 1.0 O3' A:U7 4.1 25.9 1.0 O4' A:C8 4.4 23.8 1.0 C5' A:C8 4.4 23.9 1.0 O5' A:C8 4.5 29.9 1.0 OP1 A:C8 4.7 29.3 1.0 C4' A:C8 5.0 23.8 1.0

Calcium binding site 2 out of 4 in the Cocrystal Structure of A Mutant 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 Mutant Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:26.9 occ:1.00 OP2 A:G5 2.3 26.4 1.0 O A:HOH134 2.5 28.2 1.0 O A:HOH122 2.6 29.9 1.0 O A:HOH137 2.6 25.9 1.0 O A:HOH135 2.8 16.3 1.0 O A:HOH152 2.9 41.4 1.0 O A:HOH136 3.1 33.0 1.0 P A:G5 3.7 24.2 1.0 OP1 A:G5 4.3 27.4 1.0 O5' A:G5 4.3 21.5 1.0 N7 A:G5 4.3 15.3 1.0 OP1 A:G11 4.5 24.1 1.0 O5' A:C12 4.5 36.4 1.0 C8 A:G5 4.5 27.7 1.0 O A:HOH121 4.6 17.0 1.0 OP2 A:G11 4.6 14.4 1.0 N11 A:PRF301 4.7 25.2 1.0 O A:HOH124 4.8 16.1 1.0 O3' A:G4 4.8 20.2 1.0 C10 A:PRF301 4.9 21.1 1.0

Calcium binding site 3 out of 4 in the Cocrystal Structure of A Mutant 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 Mutant Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:24.4 occ:1.00 OP2 A:U9 2.2 20.7 1.0 OP2 A:U7 2.3 24.6 1.0 O A:HOH111 2.4 19.2 1.0 O A:HOH113 2.5 22.0 1.0 O A:HOH110 2.5 22.9 1.0 O A:HOH129 2.5 28.8 1.0 O A:HOH112 3.0 17.5 1.0 P A:U9 3.5 22.0 1.0 P A:U7 3.7 26.8 1.0 OP1 A:U9 4.2 26.3 1.0 O5' A:U9 4.2 26.4 1.0 O5' A:U7 4.3 29.9 1.0 O A:HOH126 4.3 34.3 1.0 C5 A:U7 4.5 14.9 1.0 OP1 A:U7 4.5 31.1 1.0 OP2 A:A10 4.5 17.4 1.0 OP2 A:U6 4.6 22.1 1.0 O5' A:U6 4.6 32.0 1.0 C5 A:U9 4.6 23.3 1.0 O A:HOH165 4.6 41.3 1.0 O A:HOH123 4.7 35.9 1.0 O3' A:C8 4.7 21.5 1.0 O3' A:U6 4.7 28.4 1.0 C3' A:U6 4.8 17.0 1.0 C6 A:U7 4.8 22.2 1.0 O A:HOH130 4.9 32.8 1.0 O A:HOH127 4.9 42.9 1.0 C6 A:U9 4.9 18.1 1.0 P A:U6 5.0 26.5 1.0

Calcium binding site 4 out of 4 in the Cocrystal Structure of A Mutant 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 Mutant Class-I PREQ1 Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:25.9 occ:0.50 O A:HOH102 2.4 18.4 1.0 O A:HOH106 2.7 35.0 0.5 O A:HOH103 2.8 27.4 0.5 O A:HOH104 2.8 27.8 1.0 O A:HOH105 3.0 30.2 1.0 O2 A:C8 4.5 21.4 1.0 C2 A:A34 4.6 17.8 1.0 N3 A:A34 4.6 21.7 1.0 N3 A:C8 4.9 18.9 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