› 5dh7

X-ray diffraction
3.06Å resolution

Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-G12A mutant in Mn2+

Released:
DOI: 10.2210/pdb5dh7/pdb
PDB entry 5dh7 coloured by chain, front view.
PDB entry 5dh7 coloured by chain, side view.
PDB entry 5dh7 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)
Assembly name:
PDBe Complex ID:
PDB-CPX-196916 (preferred)
Entry contents:
2 distinct RNA molecules
Macromolecules (2 distinct):
RNA (48-MER) Chain: A
Molecule details ›
Chain: A
Length: 48 nucleotides
Theoretical weight: 15.48 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-R(*GP*GP*GP*CP*GP*UP*DC*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

1 bound ligand:
Ligand MN 11 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2221
Unit cell:
a: 81.309Å b: 85.825Å c: 103.528Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.2 0.252
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)