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

X-ray diffraction
2.05Å resolution
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
Assembly composition:
hetero pentamer (preferred)
Entry contents: 4 distinct RNA molecules
1 distinct DNA/RNA hybrid molecule

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero pentamer
Accessible surface area: 9066.1 Å2
Buried surface area: 6734.53 Å2
Dissociation area: 794.6 Å2
Dissociation energy (ΔGdiss): 1 kcal/mol
Dissociation entropy (TΔSdiss): 9.08 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-113106

Macromolecules

RNA chain A
Name: 5' substrate strand, pentameric fragment
Representative chains: A
Source organism: Synthetic construct [32630]
Expression system: Not provided
Length: 5 nucleotides
Theoretical weight: 1.59 KDa
5' substrate strand, pentameric fragment in PDB entry 2p7e, assembly 1, front view.
5' substrate strand, pentameric fragment in PDB entry 2p7e, assembly 1, side view.
5' substrate strand, pentameric fragment in PDB entry 2p7e, assembly 1, top view.
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RNA chain C
Name: Ribozyme strand II
Representative chains: C
Source organism: Synthetic construct [32630]
Expression system: Not provided
Length: 17 nucleotides
Theoretical weight: 5.54 KDa
Ribozyme strand II in PDB entry 2p7e, assembly 1, front view.
Ribozyme strand II in PDB entry 2p7e, assembly 1, side view.
Ribozyme strand II in PDB entry 2p7e, assembly 1, top view.
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RNA chain D
Name: Ribozyme strand III
Representative chains: D
Source organism: Synthetic construct [32630]
Expression system: Not provided
Length: 19 nucleotides
Theoretical weight: 5.99 KDa
Ribozyme strand III in PDB entry 2p7e, assembly 1, front view.
Ribozyme strand III in PDB entry 2p7e, assembly 1, side view.
Ribozyme strand III in PDB entry 2p7e, assembly 1, top view.
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RNA chain P
Name: 3' substrate strand, octameric fragment
Representative chains: P
Source organism: Synthetic construct [32630]
Expression system: Not provided
Length: 8 nucleotides
Theoretical weight: 2.5 KDa
3' substrate strand, octameric fragment in PDB entry 2p7e, assembly 1, front view.
3' substrate strand, octameric fragment in PDB entry 2p7e, assembly 1, side view.
3' substrate strand, octameric fragment in PDB entry 2p7e, assembly 1, top view.
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DNA/RNA hybrid chain B
Name: Ribozyme strand I
Representative chains: B
Source organism: Synthetic construct [32630]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 4.18 KDa
Ribozyme strand I in PDB entry 2p7e, assembly 1, front view.
Ribozyme strand I in PDB entry 2p7e, assembly 1, side view.
Ribozyme strand I in PDB entry 2p7e, assembly 1, top view.
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