1R2Y Hydrolase Dna date Sep 30, 2003
title Mutm (Fpg) Bound To 8-Oxoguanine (Oxog) Containing Dna
authors J.C.Fromme, G.L.Verdine
compound source
Molecule: 5'- D(Apgpgptpapgpapcpcptpgpgpapcpgpc)-3';
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Tpgpcpgptpcpcpap(8og) Pgptpcptpapcpc)-3';
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Mutm
Chain: A
Synonym: Fpg
Engineered: Yes
Mutation: Yes

Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Gene: Mutm
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24b
symmetry Space Group: P 21 21 21
R_factor 0.211 R_Free 0.257
length a length b length c angle alpha angle beta angle gamma
44.290 93.634 102.221 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.34 Å
ligand 8OG, ZN enzyme
related structures by homologous chain: 1L2B, 1L2C

Primary referenceDNA lesion recognition by the bacterial repair enzyme MutM., Fromme JC, Verdine GL, J Biol Chem 2003 Dec 19;278(51):51543-8. Epub 2003 Oct 1. PMID:14525999
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (1r2y.pdb1.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 1R2Y
  • CSU: Contacts of Structural Units for 1R2Y
  • Likely Quarternary Molecular Structure file(s) for 1R2Y
  • Structure Factors (205 Kb)
  • Retrieve 1R2Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1R2Y from S2C, [Save to disk]
  • Re-refined 1r2y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1R2Y 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 1R2Y
  • 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 1R2Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r2ya1, region A:135-228 [Jmol] [rasmolscript] [script source]
        - Domain d1r2ya2, region A:2-134 [Jmol] [rasmolscript] [script source]
        - Domain d1r2ya3, region A:229-274 [Jmol] [rasmolscript] [script source]
  • Fold representative 1r2y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1r2y_C] [1r2y_B] [1r2y] [1r2y_A]
  • SWISS-PROT database: [P84131]
  • Domain organization of [P84131_BACST] by SWISSPFAM
  • Domains found in 1R2Y: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 1R2Y
  • Community annotation for 1R2Y 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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