SMTL ID : 1zxn.2 (1 other biounit)

Human DNA topoisomerase IIa ATPase/ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: N.63 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: N.63, G.133 Ligands: ADP.5 No protein-ligand interaction detected (PLIP)

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

ADP.2: 21 residues within 4Å: Chain A: N.63, N.67, R.70, N.92, I.97, I.113, F.114, S.120, S.121, N.122, G.133, R.134, N.135, G.136, Y.137, G.138, A.139, K.140, T.187 Chain B: Y.6 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.63, A:N.92, A:S.121, A:S.121, A:S.121, A:N.122, A:R.134, A:N.135, A:G.136, A:A.139 Water bridges: A:E.59, A:N.63, A:N.63, A:D.66, A:N.67, A:G.138, A:G.138 Salt bridges: A:K.140 ADP.5: 21 residues within 4Å: Chain A: Y.6 Chain B: N.63, N.67, N.92, I.97, I.113, F.114, S.120, S.121, N.122, G.133, R.134, N.135, G.136, Y.137, G.138, A.139, K.140, T.187 Ligands: MG.3, SO4.4 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.63, B:D.66, B:D.66, B:N.92, B:N.92, B:S.121, B:S.121, B:S.121, B:N.122, B:R.134, B:N.135, B:G.136, B:Y.137, B:A.139, B:T.187, A:Y.6 Water bridges: B:N.63, B:G.138, B:G.138 Salt bridges: B:K.140

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

SO4.4: 8 residues within 4Å: Chain B: E.59, R.134, N.135, G.136, Y.137, G.138, K.350 Ligands: ADP.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.59, B:R.134, B:N.135, B:N.135, B:G.136, B:Y.137, B:G.138 Salt bridges: B:K.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, H. et al., Nucleotide-dependent Domain Movement in the ATPase Domain of a Human Type IIA DNA Topoisomerase. J.Biol.Chem. (2005)

Release Date

2005-08-23

Peptides

DNA topoisomerase II, alpha isozyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

DNA topoisomerase II, alpha isozyme

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