SMTL ID : 3dxu.2 (1 other biounit)

The crystal structure of core JMJD2D complexed with FE and N-oxalylglycine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.231, H.237, C.303, C.305 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.231, A:H.237, A:C.303, A:C.305 ZN.10: 4 residues within 4Å: Chain B: C.231, H.237, C.303, C.305 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.231, B:H.237, B:C.303, B:C.305

2 x FE2: FE (II) ION(Non-covalent)

FE2.2: 4 residues within 4Å: Chain A: H.185, E.187, H.273 Ligands: OGA.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.185, A:E.187, A:H.273, H2O.10 FE2.11: 4 residues within 4Å: Chain B: H.185, E.187, H.273 Ligands: OGA.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.185, B:E.187, B:H.273, H2O.24

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: P.106, K.117, N.121, W.178, K.179 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.121, A:W.178 Water bridges: A:N.121 Salt bridges: A:K.117, A:K.179 SO4.4: 4 residues within 4Å: Chain A: R.53, E.54, T.55, N.58 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.54, A:T.55 Water bridges: A:R.53, A:R.53, A:D.57, B:E.158, B:E.158, B:E.158 Salt bridges: A:R.53 SO4.5: 4 residues within 4Å: Chain A: R.116, K.117, K.120, N.121 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.121 Salt bridges: A:R.116, A:K.117, A:K.120 SO4.12: 5 residues within 4Å: Chain B: P.106, K.117, N.121, W.178, K.179 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.121, B:W.178 Water bridges: B:N.121 Salt bridges: B:K.117, B:K.179 SO4.13: 4 residues within 4Å: Chain B: R.53, E.54, T.55, N.58 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.54, B:T.55 Water bridges: B:R.53, B:R.53, B:T.55, B:D.57, B:N.58, A:E.158 Salt bridges: B:R.53 SO4.14: 4 residues within 4Å: Chain B: R.116, K.117, K.120, N.121 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.121 Salt bridges: B:R.116, B:K.117, B:K.120

2 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.6: 13 residues within 4Å: Chain A: Y.174, F.182, H.185, E.187, S.193, N.195, K.203, W.205, T.267, H.273, A.285 Ligands: FE2.2, GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.193, A:N.195 Salt bridges: A:K.203, A:H.273 OGA.15: 13 residues within 4Å: Chain B: Y.174, F.182, H.185, E.187, S.193, N.195, K.203, W.205, T.267, H.273, A.285 Ligands: FE2.11, GOL.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.193, B:N.195 Salt bridges: B:K.203, B:H.273

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: S.73, G.74, L.223, F.224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.223 GOL.8: 8 residues within 4Å: Chain A: D.23, F.24, K.143, Q.144, W.145, N.146, H.149, L.150 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.24, A:W.145, A:N.146 Water bridges: A:D.23, A:D.25, A:K.143, A:H.149 GOL.9: 7 residues within 4Å: Chain A: Y.172, Y.174, E.187, A.285, I.286, N.287 Ligands: OGA.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.174, A:A.285, A:N.287 Water bridges: A:D.132, A:E.187 GOL.16: 4 residues within 4Å: Chain B: S.73, G.74, L.223, F.224 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.223 GOL.17: 8 residues within 4Å: Chain B: D.23, F.24, K.143, Q.144, W.145, N.146, H.149, L.150 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.24, B:W.145, B:N.146 Water bridges: B:D.23, B:D.25, B:K.143, B:H.149 GOL.18: 7 residues within 4Å: Chain B: Y.172, Y.174, E.187, A.285, I.286, N.287 Ligands: OGA.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.174, B:A.285, B:N.287 Water bridges: B:D.132, B:E.187, B:E.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z. et al., The Crystal Structure of Core Jmjd2D. To be Published

Release Date

2009-07-28

Peptides

JmjC domain-containing histone demethylation protein 3D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

JmjC domain-containing histone demethylation protein 3D

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