4NY8 Transferase, Lyase Dna date Dec 10, 2013
title Dna Polymerase Beta With O6mg In The Template Base Opposite Incoming Non-Hydrolyzable Ctp With Manganese In The Active
authors M.C.Koag, K.Min, A.F.Monzingo, S.Lee
compound source
Molecule: Dna Polymerase Beta
Chain: A
Fragment: Unp Residues 10-335
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

Molecule: 5'-D(Cpcpgpapcp(6og)Ptpcpgpcpaptpcp 3';
Chain: T
Engineered: Yes
Other_details: Template

Synthetic: Yes

Molecule: 5'-D(Gpcptpgpaptpgpcpgpa)-3'
Chain: P
Engineered: Yes
Other_details: Upstream Primer

Synthetic: Yes

Molecule: 5'-D(Pgptpcpgpg)-3'
Chain: D
Engineered: Yes
Other_details: Downstream Primer

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.206 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.625 79.288 54.838 90.00 105.97 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand 0KX, 6OG, MN, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMetal-Dependent Conformational Activation Explains Highly Promutagenic Replication across O6-Methylguanine by Human DNA Polymerase beta, Koag MC, Lee S, J Am Chem Soc. 2014 Apr 2. PMID:24694247
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (4ny8.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 4NY8
  • CSU: Contacts of Structural Units for 4NY8
  • Structure Factors (153 Kb)
  • Retrieve 4NY8 in mmCIF format [Save to disk]
  • Re-refined 4ny8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NY8 in 3D
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  • 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 4NY8
  • 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 4NY8, from MSDmotif at EBI
  • Fold representative 4ny8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ny8] [4ny8_T] [4ny8_D] [4ny8_A] [4ny8_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4NY8: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4NY8
  • Community annotation for 4NY8 at PDBWiki (http://pdbwiki.org)

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