SMTL ID : 6go6.1

TdT chimera (Loop1 of pol mu) - ternary complex with downstream dsDNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

2 x DT- DT- DT- DT- DT- DG- DG- DC: DNA (5'-D(*TP*TP*TP*TP*TP*GP*GP*C)-3')(Non-functional Binders)(Non-covalent)

DT-DT-DT-DT-DT-DG-DG-DC.1: 5 residues within 4Å: Ligands: DA-DA-DA-DA-DA-DC.3, DA-DA-DA-DA-DA-DC.3, DA-DA-DA-DA-DA-DC.3, DA-DA-DA-DA-DA-DC.3, DA-DA-DA-DA-DA-DC.3 Protein-ligand interaction information (PLIP) not available DT-DT-DT-DT-DT-DG-DG-DC.2: 22 residues within 4Å: Chain A: L.79, R.83, N.281, L.282, R.283, Q.284, R.285, R.345, E.348, R.349, R.352, R.353, T.356, H.357, M.362, R.371 Ligands: DA-DA-DA-DA-DA-DC.3, DA-DA-DA-DA-DA-DC.3, DA-DA-DA-DA-DA-DC.3, DA-DA-DA-DA-DA-DC.3, DA-DA-DA-DA-DA-DC.3, DCT.6 Protein-ligand interaction information (PLIP) not available

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

DA-DA-DA-DA-DA-DC.3: 20 residues within 4Å: Chain A: Q.42, G.76, S.77, A.80, F.81, G.108, D.109, K.110, V.111 Ligands: DT-DT-DT-DT-DT-DG-DG-DC.1, DT-DT-DT-DT-DT-DG-DG-DC.1, DT-DT-DT-DT-DT-DG-DG-DC.1, DT-DT-DT-DT-DT-DG-DG-DC.1, DT-DT-DT-DT-DT-DG-DG-DC.1, DT-DT-DT-DT-DT-DG-DG-DC.1, DT-DT-DT-DT-DT-DG-DG-DC.2, DT-DT-DT-DT-DT-DG-DG-DC.2, DT-DT-DT-DT-DT-DG-DG-DC.2, DT-DT-DT-DT-DT-DG-DG-DC.2, DT-DT-DT-DT-DT-DG-DG-DC.2 Protein-ligand interaction information (PLIP) not available

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

NA.4: 3 residues within 4Å: Chain A: T.143, V.145, V.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.148

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.233, D.235 Ligands: DCT.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.233, A:D.235, H2O.4

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

DCT.6: 19 residues within 4Å: Chain A: G.222, G.223, R.226, K.228, G.231, H.232, D.233, D.235, A.279, H.280, N.281, L.282, G.340, W.341, G.343, R.345, E.348 Ligands: DT-DT-DT-DT-DT-DG-DG-DC.2, MG.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.223, A:H.232, A:D.233, A:D.233, A:A.279 Water bridges: A:R.226, A:K.228, A:K.228, A:H.232, A:D.233, A:D.235 Salt bridges: A:R.226, A:K.228, A:K.228, A:H.232, A:H.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loc'h, J. et al., Structural evidence for an intransbase selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction. J.Biol.Chem. (2019)

Release Date

2019-06-05

Peptides

DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase

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