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Structure paper

TitleJMJD5 is a human arginyl C-3 hydroxylase.
Journal, issue, pagesNat Commun, Vol. 9, Page 1180-1180, Year 2018
Publish dateNov 29, 2017 (structure data deposition date)
AuthorsWilkins, S.E. / Islam, S. / Gannon, J.M. / Markolovic, S. / Hopkinson, R.J. / Ge, W. / Schofield, C.J. / Chowdhury, R.
External linksNat Commun / PubMed:29563586
MethodsX-ray diffraction
Resolution1.12 - 2.541 Å
Structure data

PDB-6f4m:
Human JMJD5 in its apo form.
Method: X-RAY DIFFRACTION / Resolution: 1.705 Å

PDB-6f4n:
Human JMJD5 in complex with MN and 2OG.
Method: X-RAY DIFFRACTION / Resolution: 2.541 Å

PDB-6f4o:
Human JMJD5 in complex with Mn(II) and Succinate.
Method: X-RAY DIFFRACTION / Resolution: 1.28 Å

PDB-6f4p:
Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1)
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-6f4q:
Human JMJD5 (Q275C) in complex with Mn(II), NOG and RPS6-A138C (129-144) (complex-2)
Method: X-RAY DIFFRACTION / Resolution: 1.12 Å

PDB-6f4r:
Human JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-3)
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-6f4s:
Human JMJD5 (N308C) in complex with Mn(II), 2OG and RCCD1 (139-143) (complex-4)
Method: X-RAY DIFFRACTION / Resolution: 1.461 Å

PDB-6f4t:
Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)
Method: X-RAY DIFFRACTION / Resolution: 1.22 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-MN:
Unknown entry

ChemComp-AKG:
2-OXOGLUTARIC ACID

ChemComp-SIN:
SUCCINIC ACID

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

ChemComp-OGA:
N-OXALYLGLYCINE / inhibitor*YM

ChemComp-GOL:
GLYCEROL

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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