SMTL ID : 4qzf.1

Mouse Tdt, F401A mutant, in complex with a DSB substrate, C-A base pair

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

2 x DA- DA- DA- DA- DA- DC: 5'-D(*AP*AP*AP*AP*AP*C)-3'(Non-covalent)

DA-DA-DA-DA-DA-DC.1: 16 residues within 4Å: Chain A: Q.42, G.76, S.77, A.80, P.105, C.106, L.107, G.108, D.109, K.110, V.111 Ligands: DT-DT-DT-DT-DT-DG-DA.2, DT-DT-DT-DT-DT-DG-DA.2, DT-DT-DT-DT-DT-DG-DA.2, DT-DT-DT-DT-DT-DG-DA.2, DT-DT-DT-DT-DT-DG-DA.2 Protein-ligand interaction information (PLIP) not available DA-DA-DA-DA-DA-DC.3: 18 residues within 4Å: Chain A: V.145, F.146, G.147, V.148, G.149, L.150, K.151, T.152, M.178, H.232, F.295, R.322, W.340 Ligands: DT-DT-DT-DT-DT-DG-DA.2, DT-DT-DT-DT-DT-DG-DA.2, MG.5, NA.6, DCT.7 Protein-ligand interaction information (PLIP) not available

1 x DT- DT- DT- DT- DT- DG- DA: 5'-D(*TP*TP*TP*TP*TP*GP*A)-3'(Non-covalent)

DT-DT-DT-DT-DT-DG-DA.2: 17 residues within 4Å: Chain A: L.79, R.83, R.344, E.347, R.348, R.351, R.352, T.355, H.356, L.362 Ligands: DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.3, DCT.7 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.233, D.235 Ligands: DCT.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.233, A:D.235 MG.5: 5 residues within 4Å: Chain A: D.233, D.235, D.324 Ligands: DA-DA-DA-DA-DA-DC.3, DCT.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.233, A:D.324

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

NA.6: 5 residues within 4Å: Chain A: T.143, V.145, F.146, V.148 Ligands: DA-DA-DA-DA-DA-DC.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.143, A:G.147, A:V.148

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.7: 18 residues within 4Å: Chain A: G.222, G.223, R.226, K.228, T.230, G.231, H.232, D.233, D.235, G.339, W.340, G.342, R.344, E.347 Ligands: DT-DT-DT-DT-DT-DG-DA.2, DA-DA-DA-DA-DA-DC.3, MG.4, MG.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.223, A:T.230, A:H.232, A:D.233, A:D.233, A:D.235, A:R.344 Water bridges: A:K.228 Salt bridges: A:R.226, A:K.228, A:H.232, A:H.232, A:H.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gouge, J. et al., Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair. Embo J. (2015)

Release Date

2015-06-10

Peptides

DNA nucleotidylexotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA nucleotidylexotransferase

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