SMTL ID : 6gdy.1

Crystal structure of 2OG oxygenase JMJD6 (aa 1-343) in complex with Fe(II) and 2OG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: H.187, D.189, H.273 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.187, A:D.189, A:H.273, H2O.7 FE.12: 4 residues within 4Å: Chain B: H.187, D.189, H.273 Ligands: AKG.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.187, B:D.189, B:H.273, H2O.12

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 10 residues within 4Å: Chain A: Y.131, F.133, T.184, H.187, D.189, N.197, K.204, H.273, V.275 Ligands: FE.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.133, A:V.275 Hydrogen bonds: A:T.184, A:T.184, A:N.197 Salt bridges: A:H.187, A:K.204 AKG.13: 10 residues within 4Å: Chain B: Y.131, F.133, T.184, H.187, D.189, N.197, K.204, H.273, V.275 Ligands: FE.12 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.133, B:V.275 Hydrogen bonds: B:Y.131, B:N.197 Water bridges: B:T.285 Salt bridges: B:H.187, B:K.204

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: T.86, L.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.87 Water bridges: A:T.86, A:E.88

10 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain A: S.109, K.111, S.136 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.109, A:S.136, A:S.136 Water bridges: A:S.109, A:S.136, A:S.136 PO4.5: 7 residues within 4Å: Chain A: N.74, A.75, Q.76, E.77, W.79, K.151, P.153 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.75, A:E.77, A:W.79 Water bridges: A:K.151, A:K.151, A:K.154 Salt bridges: A:K.151 PO4.6: 5 residues within 4Å: Chain A: G.304, R.305, P.306, K.307, L.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.307, A:L.308 Salt bridges: A:R.305 PO4.7: 3 residues within 4Å: Chain A: K.91, R.95, E.119 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.91, A:R.95 PO4.8: 4 residues within 4Å: Chain A: K.4, R.8, K.113, Y.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.116 Salt bridges: A:R.8, A:K.113 PO4.14: 3 residues within 4Å: Chain B: S.55, V.56, K.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.56 Salt bridges: B:K.154 PO4.15: 3 residues within 4Å: Chain B: S.109, K.111, S.136 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.109, B:S.136, B:S.136, B:S.136 Salt bridges: B:K.100 PO4.16: 4 residues within 4Å: Chain B: R.305, P.306, K.307, L.308 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.305, B:K.307, B:L.308 Salt bridges: B:R.305 PO4.17: 3 residues within 4Å: Chain B: R.8, K.113, Y.116 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.116 Water bridges: B:R.8 Salt bridges: B:R.8, B:K.113 PO4.18: 7 residues within 4Å: Chain A: P.295, S.329, V.330, Q.333 Chain B: R.65, S.291, L.326 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.65 Hydrogen bonds: A:S.329, A:Q.333

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.9: 4 residues within 4Å: Chain A: K.84, R.89, R.92, K.93 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.93 Salt bridges: A:K.84, A:K.93 EPE.10: 3 residues within 4Å: Chain A: R.95, N.96, K.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.115

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: Y.67, T.211, G.269, G.270, V.296 Chain B: E.61, R.65, P.66 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.67, A:T.211, A:W.271 GOL.19: 8 residues within 4Å: Chain B: A.75, Q.76, E.77, W.79, K.151, V.152, P.153, K.154 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.75, B:E.77, B:E.77, B:K.154 Water bridges: B:K.151, B:K.151 GOL.20: 8 residues within 4Å: Chain B: R.17, W.26, S.128, P.129, L.130, Y.131, G.183, E.231 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.17, B:G.183, B:E.231 Water bridges: B:Y.131, B:G.183, B:E.231, B:E.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Islam, M.S. et al., Biochemical and structural investigations clarify the substrate selectivity of the 2-oxoglutarate oxygenase JMJD6. J.Biol.Chem. (2019)

Release Date

2019-04-03

Peptides

Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6