4DO9 Transferase Dna date Feb 09, 2012
title Ternary Complex Of Dna Polymerase Beta With A Dideoxy Termin Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethy Triphosphate: Stereoselective Binding Of R-Isomer
authors V.K.Batra
compound source
Molecule: Dna Polymerase Beta
Chain: A
Fragment: Dna Polymerase Beta
Ec:, 4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Tap56
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pwl11

Molecule: C C G A C C G C G C A T C A G C
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide

Molecule: G C T G A T G C G (Doc)
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide

Molecule: G T C G G
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide
symmetry Space Group: P 1 21 1
R_factor 0.188 R_Free 0.243
length a length b length c angle alpha angle beta angle gamma
50.693 79.914 55.607 90.00 107.66 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand CL, DOC, GFH, MG, NA enzyme Transferase E.C. BRENDA

Primary referencebeta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases., Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE, J Am Chem Soc. 2012 May 30;134(21):8734-7. Epub 2012 May 18. PMID:22397499
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (4do9.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 4DO9
  • CSU: Contacts of Structural Units for 4DO9
  • Structure Factors (338 Kb)
  • Retrieve 4DO9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DO9 from S2C, [Save to disk]
  • Re-refined 4do9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DO9 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 4DO9
  • 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 4DO9, from MSDmotif at EBI
  • Fold representative 4do9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4do9_A] [4do9] [4do9_D] [4do9_T] [4do9_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DO9: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4DO9
  • Community annotation for 4DO9 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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