› 5dqk

X-ray diffraction
2.71Å resolution

Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mg2+

Released:
DOI: 10.2210/pdb5dqk/pdb
PDB entry 5dqk coloured by chain, front view.
PDB entry 5dqk coloured by chain, side view.
PDB entry 5dqk coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.
Mir A, Chen J, Robinson K, Lendy E, Goodman J, Neau D, Golden BL
Biochemistry 54 6369-81 (2015)
PMID: 26398724

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-113172 (preferred)
Entry contents:
1 distinct RNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (2 distinct):
RNA (48-MER) Chain: A
Molecule details ›
Chain: A
Length: 48 nucleotides
Theoretical weight: 15.5 KDa
Source organism: synthetic construct
Expression system: Not provided
RNA (5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 20 nucleotides
Theoretical weight: 6.44 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand K 4 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2221
Unit cell:
a: 79.764Å b: 86.07Å c: 103.338Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.224 0.278
Expression system: Not provided

Quick links

Citations

5 review citations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Šponer et al. (2018)
4 more

1 mention without citation

Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.
Mir et al. (2015)