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Structure paper

TitleStructural analysis of the 2-oxoglutarate binding site of the circadian rhythm linked oxygenase JMJD5.
Journal, issue, pagesSci Rep, Vol. 12, Page 20680-20680, Year 2022
Publish dateNov 23, 2018 (structure data deposition date)
AuthorsIslam, M.S. / Markoulides, M. / Chowdhury, R. / Schofield, C.J.
External linksSci Rep / PubMed:36450832
MethodsX-ray diffraction
Resolution1.361 - 1.65 Å
Structure data

PDB-6i9l:
JmjC domain-containing protein 5 (JMJD5) in complex with Mn and pyridine-2,4-dicarboxylic acid (2,4-PDCA)
Method: X-RAY DIFFRACTION / Resolution: 1.53 Å

PDB-6i9m:
JmjC domain-containing protein 5 (JMJD5) in complex with Mn and R-2-hydroxyglutarate
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-6i9n:
JmjC domain-containing protein 5 (JMJD5) in complex with Mn and L-2-hydroxyglutarate
Method: X-RAY DIFFRACTION / Resolution: 1.361 Å

PDB-7uq3:
JmjC domain-containing protein 5 (JMJD5) in complex with Mn and (S)-2-(1-hydroxy-2,5-dioxopyrrolidin-3-yl)acetic acid
Method: X-RAY DIFFRACTION / Resolution: 1.49 Å

Chemicals

ChemComp-MN:
Unknown entry

ChemComp-PD2:
PYRIDINE-2,4-DICARBOXYLIC ACID

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

ChemComp-HOH:
WATER

ChemComp-2HG:
(2R)-2-hydroxypentanedioic acid

ChemComp-GOL:
GLYCEROL

ChemComp-S2G:
(2S)-2-HYDROXYPENTANEDIOIC ACID

ChemComp-O2U:
[(3S)-1-hydroxy-2,5-dioxopyrrolidin-3-yl]acetic acid

Source
  • homo sapiens (human)
KeywordsOXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / JMJC / JMJC DOMAIN / Lysine-specific demethylase 8 / JmjC domain-containing protein 5 / Arginyl C-3 Hydroxylase / JMJD5 / KDM8 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSLATION / DSBH / FACIAL TRIAD / CYTOPLASM / JMJC HYDROXYLASE / JMJC DEMETHYLASE / KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM / BETA-HYDROXYLATION / HYDROXYLATION / ARGININE HYDROXYLATION / RCC1 domain-containing protein 1 / RCCD1 / Regulator of chromosome condensation / 40S ribosomal protein S6 / RPS6 / RIBOSOME BIOGENESIS / TRANSCRIPTION / EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / TRANSCRIPTION ACTIVATOR/INHIBITOR / PHOSPHORYLATION / CANCER / POLYMORPHISM

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