2NOB	Hydrolase, Lyase Dna	date	Oct 25, 2006
title	Structure Of Catalytically Inactive H270a Human 8- Oxoguanine Glycosylase Crosslinked To 8-Oxoguanine Dna
authors	C.T.Radom, A.Banerjee, G.L.Verdine
compound		source
Molecule: 5'- D(Tgpgptpapgpapcpcptpgpgpapcpgpc)-3'; Chain: B Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Gcpgptpcpcpap(G42) Pgptpcptpapcpc)-3'; Chain: C Engineered: Yes		Synthetic: Yes
Molecule: N-Glycosylasedna Lyase Chain: A Fragment: 8-Oxoguanine Dna Glycosylase, Dna-(Apurinic Or Apyrimidinic Site) Lyase; Synonym: Ap Lyase Ec: 3.2.2.-, 4.2.99.18 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ogg1, Mmh, Mutm, Ogh1 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet30a
symmetry	Space Group: P 65 2 2	R_factor 0.225 R_Free 0.258
crystal cell	length a length b length c angle alpha angle beta angle gamma 92.359 92.359 211.726 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	8OG, CA	enzyme	Hydrolase E.C.3.2.2 BRENDA
Gene Ontology	Chain Function Process Component A damaged DNA binding catalytic activity DNA-(apurinic or apyrimidini... endonuclease activity protein binding microtubule binding oxidized purine nucleobase l... hydrolase activity hydrolase activity, acting o... lyase activity DNA N-glycosylase activity 8-oxo-7,8-dihydroguanine DNA... acute inflammatory response DNA repair base-excision repair base-excision repair, AP sit... nucleotide-excision repair regulation of transcription,... response to DNA damage stimu... response to oxidative stress... metabolic process response to radiation response to estradiol stimul... regulation of protein import... response to drug depurination response to ethanol response to folic acid cellular response to cadmium... nucleus nucleoplasm nucleolus mitochondrion nuclear matrix nuclear speck
Primary reference	Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations., Radom CT, Banerjee A, Verdine GL, J Biol Chem. 2007 Mar 23;282(12):9182-94. Epub 2006 Nov 16. PMID:17114185

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk] Biological Unit Coordinates (2nob.pdb1.gz) 66 Kb LPC: Ligand-Protein Contacts for 2NOB CSU: Contacts of Structural Units for 2NOB Likely Quarternary Molecular Structure file(s) for 2NOB Structure Factors (427 Kb) Retrieve 2NOB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2NOB from S2C, [Save to disk] Re-refined 2nob structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2NOB 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2NOB

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 2NOB, from MSDmotif at EBI Fold representative 2nob from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2nob_A] [2nob_B] [2nob_C] SWISS-PROT database: [O15527] Domain organization of [OGG1_HUMAN] by SWISSPFAM Domain found in 2NOB: [ENDO3c ] by SMART Alignments of the sequence of 2NOB with the sequences similar proteins can be viewed for 2NOB's classification [OGG1_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [OGG1_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2NOB

Community annotation for 2NOB at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2010 Bioinformatics Unit Weizmann Institute of Science

---