SMTL ID : 5ink.1

Mouse Tdp2 reaction product (5'-phosphorylated DNA)-abasic/THF-Mg2+ complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

3DR-DC-DG-DA-DA-DT-DT-DC-DG.1: 26 residues within 4Å: Chain A: P.204, A.205 Chain B: N.16, E.48, H.122, S.125, T.126, R.127, D.158, N.160, R.162, W.193, I.203, Y.207, F.211, D.244, H.245 Ligands: 3DR-DC-DG-DA-DA-DT-DT-DC-DG.2, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.2, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.2, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.2, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.2, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.2, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.2, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.2, MG.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.16, B:E.48, B:E.48, B:N.160, B:N.160 Salt bridges: B:H.122, B:H.245 3DR-DC-DG-DA-DA-DT-DT-DC-DG.2: 30 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, H.209, F.211, D.244, H.245 Chain B: L.201, R.202, I.203, P.204 Ligands: 3DR-DC-DG-DA-DA-DT-DT-DC-DG.1, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.1, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.1, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.1, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.1, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.1, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.1, 3DR-DC-DG-DA-DA-DT-DT-DC-DG.1, MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.16, A:E.48, A:E.48, A:N.160, A:D.244 Salt bridges: A:H.122, A:H.245

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: F.95, P.96, N.97, T.98, E.132, R.135, Q.136, T.139 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.95, A:N.97, A:N.97, A:T.98, A:R.135, A:T.139, A:T.139

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: N.16, E.48, D.244 Ligands: 3DR-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.2, H2O.17 MG.5: 3 residues within 4Å: Chain B: N.16, E.48 Ligands: 3DR-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.11, H2O.11, H2O.11, H2O.17

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

EPE.6: 6 residues within 4Å: Chain B: C.35, L.38, Y.39, V.231, G.232, L.233 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.39, B:G.232, B:L.233, B:E.234

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

PEG.7: 2 residues within 4Å: Chain B: I.66, I.67 No protein-ligand interaction detected (PLIP)

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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