SMTL ID : 7qfn.1

Human Topoisomerase II Beta ATPase ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 27 residues within 4Å: Chain A: E.62, N.66, A.67, N.70, R.73, N.95, K.98, I.100, I.116, F.117, T.122, S.123, S.124, N.125, G.136, R.137, N.138, G.139, Y.140, G.141, A.142, K.143, T.190, I.192 Chain B: Y.9 Ligands: SO4.2, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:E.62, A:N.66, A:N.95, A:S.124, A:S.124, A:S.124, A:N.125, A:R.137, A:N.138, A:G.139, A:A.142, A:T.190 Water bridges: A:A.67 Salt bridges: A:K.143 ADP.5: 27 residues within 4Å: Chain A: Y.9 Chain B: E.62, N.66, A.67, N.70, R.73, N.95, K.98, I.100, I.116, F.117, T.122, S.123, S.124, N.125, G.136, R.137, N.138, G.139, Y.140, G.141, A.142, K.143, T.190, I.192 Ligands: SO4.6, MG.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.66, B:N.95, B:S.124, B:S.124, B:N.125, B:R.137, B:N.138, B:G.139, B:A.142 Water bridges: B:A.67 Salt bridges: B:K.143

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 11 residues within 4Å: Chain A: K.58, E.62, G.136, R.137, N.138, G.139, Y.140, G.141, K.353 Ligands: ADP.1, MG.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.137, A:N.138, A:N.138, A:G.139, A:Y.140, A:Y.140 Salt bridges: A:K.58, A:K.353 SO4.3: 6 residues within 4Å: Chain A: A.222, R.226, G.227, V.228, N.240, G.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.227, A:V.228, A:G.241 Salt bridges: A:R.226 SO4.6: 11 residues within 4Å: Chain B: K.58, E.62, G.136, R.137, N.138, G.139, Y.140, G.141, K.353 Ligands: ADP.5, MG.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.137, B:N.138, B:N.138, B:G.139, B:Y.140, B:Y.140 Salt bridges: B:K.58, B:K.353 SO4.7: 6 residues within 4Å: Chain B: A.222, R.226, G.227, V.228, N.240, G.241 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.227, B:V.228, B:G.241 Salt bridges: B:R.226

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: E.62, N.66, G.136, G.141 Ligands: ADP.1, SO4.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.62 MG.8: 6 residues within 4Å: Chain B: E.62, N.66, G.136, G.141 Ligands: ADP.5, SO4.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ling, E.M. et al., A comprehensive structural analysis of the ATPase domain of human DNA topoisomerase II beta bound to AMPPNP, ADP, and the bisdioxopiperazine, ICRF193. Structure (2022)

Release Date

2022-05-25

Peptides

DNA topoisomerase 2-beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA topoisomerase 2-beta