SMTL ID : 5nfn.1 (1 other biounit)

JMJD7 IN COMPLEX WITH MN AND 2OG IN THE H32 FORM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.197, D.199, H.296 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.197, A:D.199, A:H.296, H2O.2 MN.5: 4 residues within 4Å: Chain B: H.197, D.199, H.296 Ligands: AKG.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.197, B:D.199, B:H.296, H2O.5

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

AKG.2: 13 residues within 4Å: Chain A: Y.146, W.186, T.194, H.197, D.199, N.203, Y.205, K.212, H.296, V.298, N.308, W.310 Ligands: MN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.186, A:Y.205, A:V.298 Hydrogen bonds: A:N.203 Salt bridges: A:K.212, A:H.296 AKG.6: 13 residues within 4Å: Chain B: Y.146, W.186, T.194, H.197, D.199, N.203, Y.205, K.212, H.296, V.298, N.308, W.310 Ligands: MN.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.186, B:W.186, B:T.194, B:Y.205, B:V.298 Hydrogen bonds: B:Y.146, B:T.194, B:T.194, B:N.203, B:Y.205, B:N.308 Salt bridges: B:K.212, B:H.296

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 2 residues within 4Å: Chain A: D.181, D.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.181, A:D.312 NO3.4: 3 residues within 4Å: Chain A: E.31, E.34 Chain B: S.327 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.31, A:E.34, B:S.327

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain B: D.181, D.312 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.312 GOL.8: 3 residues within 4Å: Chain B: A.250, M.251, E.252 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.252, B:E.252 GOL.9: 4 residues within 4Å: Chain B: S.273, Q.274, A.275, Q.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.274 Water bridges: B:A.277, B:A.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Markolovic, S. et al., (3S)-Lysyl hydroxylation of TRAFAC GTPases is catalyzed by the human Jumonji-C oxygenase JMJD7. To Be Published

Release Date

2018-03-14

Peptides

JmjC domain-containing protein 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

JmjC domain-containing protein 7

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