An Information Portal to 111558 Biological Macromolecular Structures

ALKBH2 F102A cross-linked to undamaged dsDNA
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Text Structural Genomics, Enzyme Function Initiative, Center for Eukaryotic Structural Genomics, CESG, Rossmann Fold, OXIDOREDUCTASE-DNA complex

    Polymeric Molecules

    Chain A
    Description Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 
    Mutation F102A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23322.9 
    Source Method genetically manipulated  
    Entity Name Alkylated DNA repair protein alkB homolog 2, DNA oxidative demethylase ALKBH2, Oxy DC1 
    Chain B
    Description DNA-1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 4618.1 
    Source Method synthetic  
    Chain C
    Description DNA-2 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 4572.1 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MG  MAGNESIUM ION  Mg   24.31  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A ALKB2_HUMAN Q6NS38     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    16491   Oxidoreductase Activity  Catalysis of an Oxidation Reduction (redox) Reaction a Reversible Chemical Reaction in Which the Oxidation State of an Atom or Atoms Within a Molecule Is Altered. One Substrate Acts As a Hydrogen or Electron Donor and Becomes Oxidized While the Other Acts As Hydrogen or Electron Acceptor and Becomes Reduced. 
    16706   Oxidoreductase Activity Acting On Paired Donors with Incorporation or Reduction of Molecular Oxygen 2 Oxoglutarate As One Donor and Incorporation of One Atom Each of Oxygen Into Both Donors  Catalysis of the Reaction: a + 2 Oxoglutarate + O2 = B + Succinate + Co2. This Is an Oxidation Reduction (redox) Reaction in Which Hydrogen or Electrons Are Transferred From 2 Oxoglutarate and One Other Donor and One Atom of Oxygen Is Incorporated Into Each Donor. 

  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene alkbh2, abh2
    Host Scientific Name Escherichia coli  

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    12 12q24.11 121642     alkB homolog 2, alpha-ketoglutarate-dependent dioxygenase ALKBH2    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs144722252 LS-SNP   dbSNP   A 99 V - > A Beta Ladder 37% (Exposed) 12 109527997
    rs199728859 LS-SNP   dbSNP   A 114 T - > M Beta Ladder 1% (Buried) 12 109527952
    rs143430599 LS-SNP   dbSNP   A 118 A - > G Turn 95% (Exposed) 12 109527940
    rs141737049 LS-SNP   dbSNP   A 128 T - > M Beta Ladder 65% (Exposed) 12 109527910
    rs145425095 LS-SNP   dbSNP   A 140 R - > C Helix 26% (Intermediate) 12 109527875
    rs139644396 LS-SNP   dbSNP   A 141 I - > V Helix 0% (Buried) 12 109527872
    rs141799372 LS-SNP   dbSNP   A 156 V - > G Beta Ladder 0% (Buried) 12 109527826
    rs200594471 LS-SNP   dbSNP   A 158 I - > M Beta Ladder 0% (Buried) 12 109527819
    rs144733649 LS-SNP   dbSNP   A 174 D - > G Coil 56% (Exposed) 12 109526276
    rs140769082 LS-SNP   dbSNP   A 180 P - > S Coil 0% (Buried) 12 109526259
    rs202136105 LS-SNP   dbSNP   A 198 R - > W Beta Ladder 44% (Exposed) 12 109526205
    rs150621218 LS-SNP   dbSNP   A 199 H - > R Beta Ladder 4% (Buried) 12 109526201
    rs33962311 LS-SNP   dbSNP   A 203 R - > H Coil 0% (Buried) 12 109526189
    rs148504183 LS-SNP   dbSNP   A 212 A - > V Coil 61% (Exposed) 12 109526162
    rs144639687 LS-SNP   dbSNP   A 229 P - > A Turn 25% (Intermediate) 12 109526112
    rs141848154 LS-SNP   dbSNP   A 232 T - > M Helix 23% (Intermediate) 12 109526102
    rs142477859 LS-SNP   dbSNP   A 244 V - > I Coil 23% (Intermediate) 12 109526067
    rs137964396 LS-SNP   dbSNP   A 251 L - > P Beta Ladder 0% (Buried) 12 109526045