SMTL ID : 4gz1.2 (2 other biounits)

Mus Musculus Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex at 1.5 Angstroms resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x DC- DC- DG- DA- DA- DT- DT- DC- DG: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')(Non-covalent)

DC-DC-DG-DA-DA-DT-DT-DC-DG.1: 16 residues within 4Å: Chain A: N.16, E.48, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, L.201, I.203, Y.207, F.211, H.245 Ligands: MG.3 Protein-ligand interaction information (PLIP) not available

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 5 residues within 4Å: Chain A: C.35, Y.39, V.231, G.232, L.233 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.39, A:G.232, A:L.233

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: N.16, E.48 Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.48, H2O.4, H2O.4, H2O.4, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schellenberg, M.J. et al., Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-10-31

Peptides

Tyrosyl-DNA phosphodiesterase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tyrosyl-DNA phosphodiesterase 2

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