SMTL ID : 5inq.1

Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Ca2+ complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 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: 25 residues within 4Å: Chain A: I.203, P.204, A.205 Chain B: 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 Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, DC-DC-DG-DA-DA-DT-DT-DC-DG.2, CA.5 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DA-DA-DT-DT-DC-DG.2: 24 residues within 4Å: Chain A: 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 Chain B: I.203, P.204 Ligands: DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, DC-DC-DG-DA-DA-DT-DT-DC-DG.1, CA.3 Protein-ligand interaction information (PLIP) not available

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: D.18, E.48 Ligands: DC-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.4, H2O.14 CA.5: 3 residues within 4Å: Chain B: D.18, E.48 Ligands: DC-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.9, H2O.10, H2O.11, H2O.13

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

PEG.4: 1 residues within 4Å: Chain A: P.94 No protein-ligand interaction detected (PLIP)

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

EPE.6: 6 residues within 4Å: Chain B: C.35, Y.39, V.231, G.232, L.233, E.234 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.39, B:G.232, B:L.233

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain B: F.95, P.96, N.97, T.98, E.132, R.135, Q.136, T.139 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.95, B:N.97, B:T.98, B:T.139, B:T.139

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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