Table 1.
Crystallographically determined active site structures of the JMJD2 family of histone demethylases.
| PDB | Protein | Metal ions | Cofactor | Substrate | Ref |
|---|---|---|---|---|---|
| 3RVH | JMJD2A | Ni/Zn | 8-hydroxy-3-(piperazin-1- yl)quinoline-5-carboxylic acid |
none | * |
| 2Q8E | JMJD2A | Ni/Zn | N-OG | none | 24 |
| 2P5B | JMJD2A | Fe/Zn | N-OG | H3K36Me3 peptide | 23 |
| 2PXJ | JMJD2A | Fe/Zn | N-OG | H3K36Me1 peptide | 23 |
| 2Q8C | JMJD2A | Ni/Zn | αKG | H3K9Me3 peptide | 24 |
| 2OQ6 | JMJD2A | Ni/Zn | N-OG | H3K9Me3 peptide | 25 |
| 2OQ7 | JMJD2A | Ni/Zn | N-OG | none | 25 |
| 2OS2 | JMJD2A | Ni/Zn | N-OG | H3K36Me3 peptide | 25 |
| 2OT7 | JMJD2A | Ni/Zn | N-OG | H3K9Me1 peptide | 25 |
| 2OX0 | JMJD2A | Ni/Zn | N-OG | H3K9Me2 peptide | 25 |
| 2VD7 | JMJD2A | Ni/Zn | Pyridine-2,4-dicarboxylic acid | none | * |
| 4AI9 | JMJD2A | Ni/Zn | Daminozide | none | 28 |
| 2Q8D | JMJD2A | Ni/Zn | Succinic acid | H3K36Me2 peptide | 24 |
| 2YBK | JMJD2A | Ni/Zn | (2R)-2-hydroxypentanedioic acid | none | 26 |
| 2WWJ | JMJD2A | Ni/Zn | O-benzyl-N-(carboxycarbonyl)- D-tyrosine |
none | 29 |
| 4GD4 | JMJD2A | Ni/Zn | 2-(1H–pyrazol-3-yl)pyridine-4- caboxylic acid |
none | * |
| 3PDQ | JMJD2A | Ni/Zn | 4'-[(2-aminoethyl)carbamoyl]- 2,2'-bipyridine- 4-carboxylic acid |
none | 30 |
| 2GP3 | JMJD2A | Fe/Zn | none | none | 22 |
| 2YBP | JMJD2A | Ni/Zn | (2R)-2-hydroxypentanedioic acid | H3K36Me3 peptide | 26 |
| 2YBS | JMJD2A | Ni/Zn | (2S)-2-hydroxypentanedioic acid | H3K36Me3 peptide | 26 |
| 3NJY | JMJD2A | Ni/Zn | 5-carboxy-8-hydroxyquinoline | none | 31 |
| 2GP5 | JMJD2A | Fe/Zn | αKG | none | 22 |
| 3U4S | JMJD2A | Ni/Zn | N-(carboxylcabbonyl)-D-cysteine | H3K9Me3 peptide | 32 |
| 2XML | JMJD2C | Ni/Zn | N-OG | none | * |
| 3DXU | JMJD2D | Fe/Zn | N-OG | none | * |
| 4HOO | JMJD2D | Ni/Zn | none | none | 27 |
| 3DXT | JMJD2D | Zn | none | none | * |
| 4HON | JMJD2D | Ni/Zn | αKG | H3K9Me3 peptide | 27 |
*
these crystal structures have not been published but available in the PDB.