6N2S Gene Regulation Dna date Nov 14, 2018
title Ternary Complex Crystal Structure Of Dna Polymerase Beta Wit Carboxy-Dc (5-Cac) At The Templating Position
authors V.K.Batra, S.H.Wilson
compound source
Molecule: Dna Polymerase Beta
Chain: A
Fragment: Dna Polymerase Beta
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
Expression_system_strain: Tap56
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pwl-11

Molecule: Dna (5'-D(Cpcpgpapcp(1cc) Pgpcpgpcpaptpcpapgpc)-3');
Chain: T
Fragment: Template Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-3')
Chain: P
Fragment: Primer Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Fragment: Downstream Primer Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.202 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.066 79.631 55.427 90.00 106.46 90.00
method X-Ray Diffractionresolution 2.46 Å
ligand 1CC, 1GC, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMolecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA Polymerase ss., Howard MJ, Foley KG, Shock DD, Batra VK, Wilson SH, J Biol Chem. 2019 Mar 18. pii: RA118.006809. doi: 10.1074/jbc.RA118.006809. PMID:30885943
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (6n2s.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 6N2S
  • CSU: Contacts of Structural Units for 6N2S
  • Structure Factors (143 Kb)
  • Retrieve 6N2S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6N2S from S2C, [Save to disk]
  • View 6N2S 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 6N2S
  • 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: [6n2s_A] [6n2s_P] [6n2s_D] [6n2s_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6N2S
  • Community annotation for 6N2S at PDBWiki (http://pdbwiki.org)

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