SMTL ID : 4fpv.1

Crystal structure of D. rerio TDP2 complexed with single strand DNA product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

1 x DT- DG- DC- DA- DG: DNA (5'-D(P*TP*GP*CP*AP*G)-3')(Non-covalent)

DT-DG-DC-DA-DG.1: 28 residues within 4Å: Chain A: N.17, L.21, E.49, R.103, H.123, S.126, C.127, K.128, D.159, N.161, R.163, D.164, R.191, Y.192, W.194, K.202, Y.206, V.207, S.208, R.209, C.210, F.212, H.248 Chain B: K.128, N.129, Q.130, Q.132 Ligands: MG.8 Protein-ligand interaction information (PLIP) not available

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: K.10, D.229, H.230, T.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.10, A:D.229, A:T.254 NA.5: 2 residues within 4Å: Chain B: D.229, N.256 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.229, B:N.256 Water bridges: B:T.227

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: D.164, A.165, W.181, R.191, R.211, R.214 Chain B: N.129 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.163, A:A.165, A:R.191, A:R.211, A:R.211, B:N.129 Water bridges: A:R.214, A:R.214 GOL.6: 5 residues within 4Å: Chain B: R.163, D.164, R.191, R.211, R.214 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.163, B:D.164, B:D.164, B:R.191, B:R.211, B:R.211, B:R.214, B:R.214 Water bridges: B:E.166, B:V.167, B:R.211 GOL.7: 5 residues within 4Å: Chain B: E.69, S.91, E.92, I.93, L.106 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.69, B:S.91 Water bridges: B:E.69, B:I.93

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain B: E.49 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.49, H2O.10, H2O.14, H2O.15, H2O.18 MG.8: 2 residues within 4Å: Chain A: E.49 Ligands: DT-DG-DC-DA-DG.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.49, H2O.9, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, K. et al., Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-10-31

Peptides

Tyrosyl-DNA phosphodiesterase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tyrosyl-DNA phosphodiesterase 2