SMTL ID : 5cg9.1 (1 other biounit)

NgTET1 in complex with 5mC DNA in space group P3221

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: E.114, A.148, N.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.114, A:N.151

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

AKG.2: 14 residues within 4Å: Chain A: N.160, R.170, I.171, H.175, D.177, L.186, Y.188, L.199, H.225, V.227, R.235, V.239 Chain C: C.7 Ligands: MN.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.171, A:L.186, A:L.199, A:V.227 Hydrogen bonds: A:N.160, A:Y.188 Salt bridges: A:R.170, A:H.175, A:R.235

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

MN.3: 4 residues within 4Å: Chain A: H.175, D.177, H.225 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.175, A:D.177, A:H.225, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hashimoto, H. et al., Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA. Nucleic Acids Res. (2015)

Release Date

2015-09-09

Peptides

Tet-like dioxygenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tet-like dioxygenase

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