SMTL ID : 5ht2.1

Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex with 1-N6-etheno-adenine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

2 x EDA- DC- DG- DA- DA- DT- DT- DC- DG: DNA(Non-covalent)

EDA-DC-DG-DA-DA-DT-DT-DC-DG.1: 31 residues within 4Å: Chain A: I.203, P.204, A.205, Y.207 Chain B: N.16, E.48, R.102, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, L.201, I.203, A.205, Y.207, H.209, F.211, H.245 Ligands: EDA-DC-DG-DA-DA-DT-DT-DC-DG.2, EDA-DC-DG-DA-DA-DT-DT-DC-DG.2, EDA-DC-DG-DA-DA-DT-DT-DC-DG.2, EDA-DC-DG-DA-DA-DT-DT-DC-DG.2, EDA-DC-DG-DA-DA-DT-DT-DC-DG.2, EDA-DC-DG-DA-DA-DT-DT-DC-DG.2, EDA-DC-DG-DA-DA-DT-DT-DC-DG.2, EDA-DC-DG-DA-DA-DT-DT-DC-DG.2, MG.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.16, B:E.48, B:S.125, B:D.158, B:D.158, B:N.160, B:W.193, B:D.244 Salt bridges: B:H.122, B:H.245 EDA-DC-DG-DA-DA-DT-DT-DC-DG.2: 33 residues within 4Å: Chain A: N.16, E.48, R.102, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, L.201, I.203, A.205, Y.207, H.209, F.211, H.245 Chain B: K.99, E.128, I.203, P.204, A.205, Y.207 Ligands: EDA-DC-DG-DA-DA-DT-DT-DC-DG.1, EDA-DC-DG-DA-DA-DT-DT-DC-DG.1, EDA-DC-DG-DA-DA-DT-DT-DC-DG.1, EDA-DC-DG-DA-DA-DT-DT-DC-DG.1, EDA-DC-DG-DA-DA-DT-DT-DC-DG.1, EDA-DC-DG-DA-DA-DT-DT-DC-DG.1, EDA-DC-DG-DA-DA-DT-DT-DC-DG.1, EDA-DC-DG-DA-DA-DT-DT-DC-DG.1, MG.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.16, A:E.48, A:S.125, A:D.158, A:D.158, A:N.160, A:W.193, A:D.244 Salt bridges: A:H.122, A:H.245

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: N.16, E.48, H.245 Ligands: EDA-DC-DG-DA-DA-DT-DT-DC-DG.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.48, H2O.1, H2O.2, H2O.3, H2O.27 MG.4: 4 residues within 4Å: Chain B: N.16, E.48, H.245 Ligands: EDA-DC-DG-DA-DA-DT-DT-DC-DG.1 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.48, H2O.15, H2O.16, H2O.17, H2O.26 MG.7: 2 residues within 4Å: Chain B: Q.226, S.227 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:Q.226, H2O.15, H2O.21, H2O.22, H2O.25

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 8 residues within 4Å: Chain B: S.34, C.35, L.38, Y.39, V.231, G.232, L.233, E.234 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.34, B:Y.39, B:Y.39, B:G.232, B:L.233 Water bridges: B:E.234 Salt bridges: B:E.234, B:E.234

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 4 residues within 4Å: Chain B: T.65, I.66, I.67, F.87 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schellenberg, M.J. et al., Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2. Nucleic Acids Res. (2016)

Release Date

2016-04-27

Peptides

Tyrosyl-DNA phosphodiesterase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tyrosyl-DNA phosphodiesterase 2

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