6UR2 Replication Dna date Oct 21, 2019
title Dna Polymerase I Large Fragment From Bacillus Stearothermoph Dna Template And Primer Containing An N3'-> P5' Linkage
authors W.Zhang, V.S.Lelyveld, J.W.Szostak
compound source
Molecule: Dna Polymerase I
Chain: A
Ec: 2.7.7.7
Engineered: Yes
 Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Strain: Strain X
Gene: Dpo1, Pola
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Gpcpgpaptpcpapgp(C42)Pg)-3')
Chain: B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Papcpgpcptpgpaptpcpgpcpa)-3
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.229 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.197 93.679 107.140 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.27 Å
ligand C42 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • 3'-5' exonuclease activity


    • Primary referenceSynthesis of phosphoramidate-linked DNA by a modified DNA polymerase., Lelyveld VS, Zhang W, Szostak JW, Proc Natl Acad Sci U S A. 2020 Mar 31;117(13):7276-7283. doi:, 10.1073/pnas.1922400117. Epub 2020 Mar 18. PMID:32188786
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk]
  • Biological Unit Coordinates (6ur2.pdb1.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 6UR2
  • CSU: Contacts of Structural Units for 6UR2
  • Structure Factors (1147 Kb)
  • Retrieve 6UR2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6UR2 from S2C, [Save to disk]
    • View 6UR2 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 6UR2
  • 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: [6ur2_C] [6ur2_A] [6ur2_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6UR2
  • Community annotation for 6UR2 at PDBWiki (http://pdbwiki.org)

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