SMTL ID : 5nfo.1

Human JMJD7 in complex with Mn and 2OG in the P21212 form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 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.4 MN.7: 4 residues within 4Å: Chain B: H.197, D.199, H.296 Ligands: AKG.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.197, B:D.199, B:H.296, H2O.10

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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.186, A:T.194, A:Y.205, A:V.298 Hydrogen bonds: A:T.194, A:T.194, A:N.203 Water bridges: A:K.212, A:K.212 Salt bridges: A:K.212, A:H.296 AKG.8: 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.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.186, B:T.194, B:Y.205, B:V.298 Hydrogen bonds: B:T.194, B:N.203 Water bridges: B:K.212 Salt bridges: B:K.212, B:H.296

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: A.112, V.113, R.114, S.195, W.256, I.257, P.258 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:V.113, A:R.114, A:S.195, A:W.256 Water bridges: A:R.114, A:L.196, A:L.196, A:D.260 GOL.4: 6 residues within 4Å: Chain A: K.198, R.222, Y.227, P.255, D.326, K.330 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.198, A:K.198, A:R.222, A:D.326, A:K.330 GOL.5: 1 residues within 4Å: Chain A: Y.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.319 Water bridges: A:Y.319 GOL.9: 8 residues within 4Å: Chain A: C.66 Chain B: Y.61, V.65, E.202, M.313, E.314, D.316, K.318 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.202, B:E.202, B:E.314, B:K.318 Water bridges: B:D.312, B:D.316, B:K.318, A:C.66 GOL.10: 5 residues within 4Å: Chain B: R.222, Y.227, P.255, D.326, K.330 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.222, B:D.326, B:K.330 GOL.11: 8 residues within 4Å: Chain B: A.112, V.113, R.114, S.195, I.257, P.258, L.259, D.260 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.113, B:R.114, B:R.114, B:S.195, B:S.195

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

NO3.6: 5 residues within 4Å: Chain A: R.40, S.273, Q.274, A.275, Q.276 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.273, A:Q.276 Water bridges: A:R.40, A:R.40, A:R.40, A:Q.276 NO3.12: 4 residues within 4Å: Chain B: E.123, R.124, Q.236, L.237 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.123, B:R.124, B:L.237, B:L.237

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