› 2p7e

X-ray diffraction
2.05Å resolution

Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization

Released:
DOI: 10.2210/pdb2p7e/pdb
PDB entry 2p7e coloured by chain, front view.
PDB entry 2p7e coloured by chain, side view.
PDB entry 2p7e coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
Torelli AT, Krucinska J, Wedekind JE
RNA 13 1052-70 (2007)
PMID: 17488874

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-113106 (preferred)
Entry contents:
4 distinct RNA molecules
1 distinct DNA/RNA hybrid molecule
Macromolecules (5 distinct):
5' substrate strand, pentameric fragment Chain: A
Molecule details ›
Chain: A
Length: 5 nucleotides
Theoretical weight: 1.59 KDa
Source organism: Synthetic construct
Expression system: Not provided
Ribozyme strand II Chain: C
Molecule details ›
Chain: C
Length: 17 nucleotides
Theoretical weight: 5.54 KDa
Source organism: Synthetic construct
Expression system: Not provided
Ribozyme strand III Chain: D
Molecule details ›
Chain: D
Length: 19 nucleotides
Theoretical weight: 5.99 KDa
Source organism: Synthetic construct
Expression system: Not provided
3' substrate strand, octameric fragment Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.5 KDa
Source organism: Synthetic construct
Expression system: Not provided
Ribozyme strand I Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.18 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand NCO 2 x NCO
1 modified residue:
Ligand AVC 1 x AVC

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: P6122
Unit cell:
a: 94.1Å b: 94.1Å c: 132.4Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.259 0.258 0.271
Expression system: Not provided

Quick links

Citations

8 review citations

Comparative enzymology and structural biology of RNA self-cleavage.
Fedor MJ. (2009)
7 more

6 mentions without citation

A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
Torelli et al. (2007)
5 more