SMTL ID : 5deu.1

Crystal structure of TET2-5hmC complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

OGA.1: 13 residues within 4Å: Chain A: R.135, C.248, H.256, D.258, V.269, H.290, H.407, T.409, R.422, S.424, V.426 Chain B: X.6 Ligands: FE.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.424 Water bridges: A:R.422, A:S.424 Salt bridges: A:R.135, A:H.256, A:H.290, A:R.422

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 8 residues within 4Å: Chain A: E.60, E.141, A.255, H.256, R.257, L.259, L.406 Chain C: G.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.257 Salt bridges: A:R.257

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

FE.3: 4 residues within 4Å: Chain A: H.256, D.258, H.407 Ligands: OGA.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.256, A:D.258, A:H.407, H2O.1

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.7, C.9, H.93, C.95 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.7, A:C.9, A:H.93, A:C.95 ZN.5: 4 residues within 4Å: Chain A: C.67, C.145, C.147, H.254 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.145, A:C.147, A:H.254 ZN.6: 4 residues within 4Å: Chain A: C.163, C.172, C.232, H.438 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.163, A:C.172, A:C.232, A:H.438

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

CL.7: 7 residues within 4Å: Chain A: N.261, G.265, S.266, T.267, C.401, A.402, K.403 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, L. et al., Structural insight into substrate preference for TET-mediated oxidation. Nature (2015)

Release Date

2015-11-04

Peptides

Methylcytosine dioxygenase TET2, chimeric construct: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methylcytosine dioxygenase TET2, chimeric construct

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