SMTL ID : 5zqf.1

Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA in space group P3221

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.87 Å

Oligo State

homo-dimer

Ligands

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

DA-DG-DC-DC-DG-DA-DG-DC.1: 28 residues within 4Å: Chain A: E.59, G.86, K.87, S.95, D.143, R.311, K.321, Q.324, Y.355, H.357, G.358, A.361, T.365, N.368, K.396, E.452, I.454, R.527, W.529 Ligands: DA-DG-DC-IU-DC-DG-DG-DC-IU.2, DA-DG-DC-IU-DC-DG-DG-DC-IU.2, DA-DG-DC-IU-DC-DG-DG-DC-IU.2, DA-DG-DC-IU-DC-DG-DG-DC-IU.2, DA-DG-DC-IU-DC-DG-DG-DC-IU.2, DA-DG-DC-IU-DC-DG-DG-DC-IU.2, DA-DG-DC-IU-DC-DG-DG-DC-IU.2, DA-DG-DC-IU-DC-DG-DG-DC-IU.2, DA-DG-DC-IU-DC-DG-DG-DC-IU.2 Protein-ligand interaction information (PLIP) not available DA-DG-DC-DC-DG-DA-DG-DC.5: 28 residues within 4Å: Chain B: E.59, G.86, K.87, S.95, D.143, R.311, K.321, Q.324, Y.355, H.357, G.358, A.361, T.365, N.368, K.396, E.452, I.454, R.527, W.529 Ligands: DA-DG-DC-IU-DC-DG-DG-DC-IU.6, DA-DG-DC-IU-DC-DG-DG-DC-IU.6, DA-DG-DC-IU-DC-DG-DG-DC-IU.6, DA-DG-DC-IU-DC-DG-DG-DC-IU.6, DA-DG-DC-IU-DC-DG-DG-DC-IU.6, DA-DG-DC-IU-DC-DG-DG-DC-IU.6, DA-DG-DC-IU-DC-DG-DG-DC-IU.6, DA-DG-DC-IU-DC-DG-DG-DC-IU.6, DA-DG-DC-IU-DC-DG-DG-DC-IU.6 Protein-ligand interaction information (PLIP) not available

2 x DA- DG- DC- IU- DC- DG- DG- DC- IU: DNA/RNA (5'-D(P*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')(Non-covalent)

DA-DG-DC-IU-DC-DG-DG-DC-IU.2: 33 residues within 4Å: Chain A: R.85, G.86, K.87, I.88, L.89, N.90, Q.98, N.102, H.146, F.251, I.256, R.259, K.260, I.454, G.455, T.456, G.457, W.458, A.459, T.592, L.593, T.594, C.595, N.596, S.597 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.1, DA-DG-DC-DC-DG-DA-DG-DC.1, DA-DG-DC-DC-DG-DA-DG-DC.1, DA-DG-DC-DC-DG-DA-DG-DC.1, DA-DG-DC-DC-DG-DA-DG-DC.1, DA-DG-DC-DC-DG-DA-DG-DC.1, DA-DG-DC-DC-DG-DA-DG-DC.1, DA-DG-DC-DC-DG-DA-DG-DC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.592, A:T.594 DA-DG-DC-IU-DC-DG-DG-DC-IU.6: 33 residues within 4Å: Chain B: R.85, G.86, K.87, I.88, L.89, N.90, Q.98, N.102, H.146, F.251, I.256, R.259, K.260, I.454, G.455, T.456, G.457, W.458, A.459, T.592, L.593, T.594, C.595, N.596, S.597 Ligands: DA-DG-DC-DC-DG-DA-DG-DC.5, DA-DG-DC-DC-DG-DA-DG-DC.5, DA-DG-DC-DC-DG-DA-DG-DC.5, DA-DG-DC-DC-DG-DA-DG-DC.5, DA-DG-DC-DC-DG-DA-DG-DC.5, DA-DG-DC-DC-DG-DA-DG-DC.5, DA-DG-DC-DC-DG-DA-DG-DC.5, DA-DG-DC-DC-DG-DA-DG-DC.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.592, B:T.594

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

MN.3: 3 residues within 4Å: Chain A: E.59, D.139, D.141 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.139, A:D.141 MN.4: 3 residues within 4Å: Chain A: S.376, N.449, G.450 No protein-ligand interaction detected (PLIP) MN.7: 3 residues within 4Å: Chain B: E.59, D.139, D.141 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.139, B:D.141 MN.8: 3 residues within 4Å: Chain B: S.376, N.449, G.450 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S.F. et al., Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate. Nat Commun (2018)

Release Date

2018-08-08

Peptides

DNA topoisomerase 2-beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA topoisomerase 2-beta

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