SMTL ID : 4gfh.1

Topoisomerase II-DNA-AMPPNP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.41 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.66, N.70 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain F: E.66, N.70 Ligands: ANP.4 No protein-ligand interaction detected (PLIP)

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 25 residues within 4Å: Chain A: E.66, N.70, N.74, R.77, N.99, I.104, I.120, F.121, T.126, S.127, S.128, N.129, G.139, G.140, R.141, N.142, G.143, Y.144, G.145, A.146, K.147, T.195, Q.365, K.367 Ligands: MG.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.70, A:N.99, A:N.99, A:S.127, A:S.128, A:S.128, A:N.129, A:R.141, A:N.142, A:G.143, A:Y.144, A:Y.144, A:G.145, A:A.146, A:T.195, A:Q.365, A:K.367, A:K.367 Salt bridges: A:K.147 ANP.4: 25 residues within 4Å: Chain F: E.66, N.70, N.74, R.77, N.99, I.104, I.120, F.121, T.126, S.127, S.128, N.129, G.139, G.140, R.141, N.142, G.143, Y.144, G.145, A.146, K.147, T.195, Q.365, K.367 Ligands: MG.3 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:N.70, F:N.99, F:N.99, F:S.127, F:S.128, F:S.128, F:N.129, F:R.141, F:N.142, F:G.143, F:Y.144, F:G.145, F:A.146, F:Q.365, F:K.367, F:K.367, F:K.367 Salt bridges: F:K.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, B.H. et al., Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-10-03

Peptides

DNA topoisomerase 2: AF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
F

DNA topoisomerase 2