2OQ4 Hydrolase Dna date Jan 31, 2007
title Crystal Structure Of The Dna Repair Enzyme Endonuclease- Viii (Nei) From E. Coli (E2q) In Complex With Ap-Site Containing Dna Substrate
authors G.Golan, D.O.Zharkov, A.P.Grollman, G.Shoahm
compound source
Molecule: Endonuclease Viii
Chain: A, B
Synonym: Dna Glycosylaseap Lyase Nei, Dna-Apurinic Or Apyrimidinic Site, Lyase Nei;
Ec: 3.2.2.-,
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Nei
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet13a

Molecule: 5'-D(Ggpcptptpcpaptpcpcptpgpg)-3'
Chain: C, E
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Ccpapgpgpap(Ped)Pgpapapgpcpc)- 3';
Chain: D, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 43 21 2
R_factor 0.374 R_Free 0.432
length a length b length c angle alpha angle beta angle gamma
107.130 107.130 164.860 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand NA, PED, SO4, ZN enzyme Hydrolase E.C.3.2.2 BRENDA
A, B
  • endonuclease activity

  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (2oq4.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (2oq4.pdb2.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 2OQ4
  • CSU: Contacts of Structural Units for 2OQ4
  • Likely Quarternary Molecular Structure file(s) for 2OQ4
  • Retrieve 2OQ4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OQ4 from S2C, [Save to disk]
  • View 2OQ4 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 2OQ4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2OQ4, from MSDmotif at EBI
  • Fold representative 2oq4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2oq4_D] [2oq4_C] [2oq4_A] [2oq4_F] [2oq4] [2oq4_E] [2oq4_B]
  • SWISS-PROT database: [P50465]
  • Domain organization of [END8_ECOLI] by SWISSPFAM
  • Domains found in 2OQ4: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 2OQ4
  • Community annotation for 2OQ4 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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