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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature 439 879-884 2006
    Site NESGC
    PDB Id 2fd8 Target Id ER126
    Related PDB Ids 2fdk 2fdj 2fdi 2fdh 2fdg 2fdf 
    Molecular Characteristics
    Source Escherichia coli
    Alias Ids TPS8826,, BIG_205 Molecular Weight 24074.24 Da.
    Residues 216 Isoelectric Point 7.73
    Sequence mldlfadaepwqeplaagavilrrfafnaaeqlirdindvasqspfrqmvtpggytmsvamtncghlgw tthrqgylyspidpqtnkpwpampqsfhnlcqraataagypdfqpdaclinryapgaklslhqdkdepd lrapivsvslglpaifqfgglkrndplkrlllehgdvvvwggesrlfyhgiqplkagfhpltidcrynl tfrqagkke
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.30 Rfree 0.227
    Matthews' coefficent 2.00 Rfactor 0.186
    Waters 214 Solvent Content 38.58

    Ligand Information
    Ligands AKG (2-OXYGLUTARIC) x 1
    Metals FE2 (FE) x 1


    Google Scholar output for 2fd8
    1. Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids
    LM Iyer, M Tahiliani, A Rao - Cell cycle (Georgetown, , 2009 - ncbi.nlm.nih.gov
    2. The active site of an algal prolyl 4-hydroxylase has a large structural plasticity
    MK Koski, R Hieta, C Bllner, KI Kivirikko - Journal of Biological , 2007 - ASBMB
    3. Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase
    LM Iyer, S Abhiman, RF de Souza - Nucleic acids , 2010 - Oxford Univ Press
    4. FeII/_-ketoglutarate hydroxylases involved in nucleobase, nucleoside, nucleotide, and chromatin metabolism
    JM Simmons, TA Mller, RP Hausinger - Dalton Trans., 2008 - xlink.rsc.org
    5. Mechanistics of Enzyme Catalysis: From Small to Large Active_Site Models
    J Llano, JW Gauld - Quantum Biochemistry, 2010 - Wiley Online Library
    6. A DFT study of nucleobase dealkylation by the DNA repair enzyme AlkB
    H Liu, J Llano, JW Gauld - The Journal of Physical Chemistry B, 2009 - ACS Publications
    7. Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching
    PJ Holland, T Hollis - PloS one, 2010 - dx.plos.org
    8. Crystal structure of prolyl 4-hydroxylase from Bacillus anthracis
    MA Culpepper, EE Scott, J Limburg - Biochemistry, 2009 - ACS Publications
    9. Cloning and characterization of Rhodotorula glutinis thymine hydroxylase
    JW Neidigh, A Darwanto, AA Williams - Chemical research in , 2009 - ACS Publications
    10. Replacement of non-heme Fe (II) with Cu (II) in the _-ketoglutarate dependent DNA repair enzyme AlkB: Spectroscopic characterization of the active site
    B Bleijlevens, T Shivarattan, B Sedgwick - Journal of inorganic , 2007 - Elsevier
    11. A mixture of fortunes: the curious determination of the structure of Escherichia coli BL21 Gab protein
    B Lohkamp, D Dobritzsch - Acta Crystallographica Section D: , 2008 - scripts.iucr.org
    12. Dynamic Combinatorial Mass Spectrometry Leads to Inhibitors of a 2-Oxoglutarate Dependent Nucleic Acid Demethylase
    ECY Woon, M Demetriades, EAL Bagg - Journal of Medicinal , 2012 - ACS Publications
    13. Applications of Potential Energy Surfaces in the Study of Enzymatic Reactions
    EAC Bushnell, WJ Huang, JW Gauld - Advances in Physical Chemistry, 2011 - hindawi.com
    14. Quantitative Assessment of Protein Structural Models by Comparison of H/D Exchange MS Data with Exchange Behavior Accurately Predicted by DXCOREX
    T Liu, D Pantazatos, S Li, Y Hamuro, VJ Hilser - Journal of the American , 2011 - Springer

    Protein Summary

    Ligand Summary




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