4RQ5 Transferase Dna date Oct 31, 2014
title Human Dna Polymerase Beta With Gapped Dna Containing An 8-Ox Dihydro-Guanine (8-Oxog)And Datp Soaked With Mgcl2 For 60 S
authors R.Vyas, Z.Suo
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7, 4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pol B, Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Synonym: 5-Mer Phosphorylated Downstream Primer
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpcpa)-3')
Chain: P
Synonym: 10-Mer Primer
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Cpcpgpapcp(8og) Pgpcpgpcpaptpcpapgpc)-3');
Chain: T
Synonym: 16-Mer Template
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.196 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.212 79.702 55.384 90.00 106.66 90.00
method X-Ray Diffractionresolution 2.32 Å
ligand 8OG, ACT, CL, DTP, MG, NA, PPV enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceViewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography., Vyas R, Reed AJ, Tokarsky EJ, Suo Z, J Am Chem Soc. 2015 Apr 9. PMID:25825995
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (4rq5.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 4RQ5
  • CSU: Contacts of Structural Units for 4RQ5
  • Structure Factors (334 Kb)
  • Retrieve 4RQ5 in mmCIF format [Save to disk]
  • Re-refined 4rq5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4RQ5 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 4RQ5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4RQ5, from MSDmotif at EBI
  • Fold representative 4rq5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rq5_D] [4rq5_P] [4rq5_A] [4rq5] [4rq5_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4RQ5: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4RQ5
  • Community annotation for 4RQ5 at PDBWiki (http://pdbwiki.org)

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