› 6cc1

X-ray diffraction
2.54Å resolution

Crystal structure of ykoY-alx riboswitch chimera bound to cadmium

Released:
DOI: 10.2210/pdb6cc1/pdb
PDB entry 6cc1 coloured by chain, front view.
PDB entry 6cc1 coloured by chain, side view.
PDB entry 6cc1 coloured by chain, top view.
Source organism: Lactococcus lactis
Primary publication:
Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators.
Bachas ST, Ferré-D'Amaré AR
Cell Chem Biol 25 962-973.e5 (2018)
PMID: 29805037

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195847 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
RNA (94-MER) Chains: A, B
Molecule details ›
Chains: A, B
Length: 101 nucleotides
Theoretical weight: 32.65 KDa
Source organism: Lactococcus lactis
Expression system: Not provided
Sequence domains: yybP-ykoY manganese riboswitch

Ligands and Environments

4 bound ligands:
Ligand CD 23 x CD
Ligand BA 8 x BA
Ligand MG 1 x MG
Ligand GTP 2 x GTP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P31
Unit cell:
a: 73.089Å b: 73.089Å c: 117.082Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.229 0.222 0.281
Expression system: Not provided

Quick links

Citations

3 review citations

Discovering riboswitches: the past and the future.
Kavita et al. (2023)
2 more

2 mentions without citation

Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators.
Bachas et al. (2018)
1 more