4Z6C Transferase Dna date Apr 04, 2015
title Structure Of Human Dna Polymerase Beta 279na Mutant Complexe In The Template Base Paired With Incoming Non-Hydrolyzable
authors M.C.Koag, S.Lee
compound source
Molecule: Dna (5'-D(Cpcpgpapcpgptpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpa)-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.201 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.180 79.274 54.372 90.00 105.96 90.00
method X-Ray Diffractionresolution 2.68 Å
ligand 0KX, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceInsights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase beta., Koag MC, Lee S, Biochem J. 2018 Feb 9;475(3):571-585. doi: 10.1042/BCJ20170787. PMID:29301983
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (4z6c.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 4Z6C
  • CSU: Contacts of Structural Units for 4Z6C
  • Structure Factors (106 Kb)
  • Retrieve 4Z6C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Z6C from S2C, [Save to disk]
  • Re-refined 4z6c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Z6C 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 4Z6C
  • 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
  • Fold representative 4z6c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4z6c_P] [4z6c] [4z6c_D] [4z6c_T] [4z6c_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4Z6C: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4Z6C
  • Community annotation for 4Z6C at PDBWiki (http://pdbwiki.org)

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