5DH7 Rna date Aug 29, 2015
title Two Divalent Metal Ions And Conformational Changes Play Role Hammerhead Ribozyme Cleavage Reaction-G12a Mutant In Mn2+
authors A.Mir, J.Chen, D.Neau, B.L.Golden
compound source
Molecule: Rna (48-Mer)
Chain: A
Engineered: Yes
Mutation: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: This Rna Was Made By In Vitro Transcription

Molecule: 5'-R(Gpgpgpcpgpupdcupgpgpgpcpapgpu Cpa)-3';
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthesized Oligonucleotide
symmetry Space Group: C 2 2 21
R_factor 0.200 R_Free 0.252
length a length b length c angle alpha angle beta angle gamma
81.309 85.825 103.528 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.06 Å
ligand MN enzyme
Primary referenceTwo 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. 2015 Oct 2. PMID:26398724
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (5dh7.pdb1.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 5DH7
  • CSU: Contacts of Structural Units for 5DH7
  • Structure Factors (169 Kb)
  • Retrieve 5DH7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DH7 from S2C, [Save to disk]
  • Re-refined 5dh7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DH7 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5DH7
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dh7_B] [5dh7] [5dh7_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5DH7
  • Community annotation for 5DH7 at PDBWiki (http://pdbwiki.org)

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