4NM2 Transferase, Lyase Dna date Nov 14, 2013
title Structure Of Human Dna Polymerase Beta Complexed With A Nick Containing A 8brg-G At N-1 Position And G-C At N Position
authors M.C.Koag, K.Min, A.F.Monzingo, S.Lee
compound source
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

Molecule: 5'-D(Cpcpgpapcpgp(Bgm)Pcpgpcpaptpcp 3';
Chain: T
Engineered: Yes
Other_details: Template

Synthetic: Yes

Molecule: 5'-D(Gpcptpgpaptpgpcpgpgpc)-3'
Chain: P
Engineered: Yes
Other_details: Up Primer

Synthetic: Yes

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

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.200 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.731 80.202 55.109 90.00 106.60 90.00
method X-Ray Diffractionresolution 2.52 Å
ligand BGM, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for promutagenicity of 8-halogenated guanine., Koag MC, Min K, Lee S, J Biol Chem. 2014 Jan 14. PMID:24425881
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (133 Kb) [Save to disk]
  • Biological Unit Coordinates (4nm2.pdb1.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 4NM2
  • CSU: Contacts of Structural Units for 4NM2
  • Structure Factors (107 Kb)
  • Retrieve 4NM2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NM2 from S2C, [Save to disk]
  • Re-refined 4nm2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NM2 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 4NM2
  • 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 4NM2, from MSDmotif at EBI
  • Fold representative 4nm2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nm2_P] [4nm2] [4nm2_A] [4nm2_D] [4nm2_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4NM2: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4NM2
  • Community annotation for 4NM2 at PDBWiki (http://pdbwiki.org)

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