SMTL ID : 4v2w.1 (1 other biounit)

JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 6 residues within 4Å: Chain A: H.210, E.212, S.218, H.298 Chain B: K.12 Ligands: OGA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.6

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: C.256, F.259, H.262, C.328, S.329, C.330, R.331 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.256, A:H.262, A:C.328, A:C.330

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 Ligand excluded by PLIP

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

OGA.4: 15 residues within 4Å: Chain A: Y.154, Y.199, F.207, H.210, E.212, S.218, N.220, K.228, W.230, T.292, H.298, A.308, S.310 Chain B: K.12 Ligands: NI.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.154, A:S.218, A:N.220 Salt bridges: A:K.228, A:H.298

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: Y.81, D.82, I.84, R.120, F.224, F.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.120 Water bridges: A:D.82, A:G.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, S.T. et al., Studies on the Catalytic Domains of Multiple Jmjc Oxygenases Using Peptide Substrates. Epigenetics (2014)

Release Date

2014-11-26

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A
HISTONE H3.1T: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

LYSINE-SPECIFIC DEMETHYLASE 4A

HISTONE H3.1T

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