3LZI Transferase Dna date Mar 01, 2010
title Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp Opposi Dihydro-8-Oxoguanine
authors M.Wang, J.Beckman, G.Blaha, J.Wang, W.H.Konigsberg
compound source
Molecule: Dna Polymerase
Chain: A
Synonym: Gp43
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_common: Bacteriophage Rb69
Organism_taxid: 12353
Gene: 43, Gp43
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet 21b

Molecule: Dna (5'-D(Ptpcpap(8og) Pgptpapapgpcpapgptpcpcpgpcpg)-3');
Chain: T
Engineered: Yes
Other_details: Template Dna Strand

Synthetic: Yes

Molecule: Dna (5'-D(Gpcpgpgpapcptpgpcptptpap(D
Chain: P
Engineered: Yes
Other_details: Primer Dna Strand

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.206 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.148 117.603 130.681 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 8OG, CA, DOC, DTP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


  • Primary referenceSubstitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine ., Beckman J, Wang M, Blaha G, Wang J, Konigsberg WH, Biochemistry. 2010 May 18;49(19):4116-25. PMID:20411947
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (175 Kb) [Save to disk]
  • Biological Unit Coordinates (3lzi.pdb1.gz) 167 Kb
  • LPC: Ligand-Protein Contacts for 3LZI
  • CSU: Contacts of Structural Units for 3LZI
  • Structure Factors (803 Kb)
  • Retrieve 3LZI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LZI from S2C, [Save to disk]
  • Re-refined 3lzi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LZI 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 3LZI
  • 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 3LZI, from MSDmotif at EBI
  • Fold representative 3lzi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lzi_A] [3lzi_P] [3lzi_T] [3lzi]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LZI: [POLBc ] by SMART
  • Other resources with information on 3LZI
  • Community annotation for 3LZI at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
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