SMTL ID : 6go5.2 (1 other biounit)

TdT chimera (Loop1 of pol mu) - Ternary complex with 1-nt gapped DNA substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

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

DT-DG-DT-DT-DT-DG.1: 24 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, D.233, D.235, R.294, F.296, R.323, D.325 Chain B: C.7, A.8, A.9, A.10, C.11, A.12 Ligands: NA.4, XC5.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.76, A:R.83, A:R.83, A:Q.177, A:Q.269, A:H.271, A:R.272, A:R.345 Water bridges: A:G.76 Salt bridges: A:R.83, A:R.349, A:H.357

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

DA-DC-DA-DG-DC-DG.2: 17 residues within 4Å: Chain A: Q.42, G.76, S.77, A.80, F.81, P.105, C.106, L.107, G.108, D.109, K.110, V.111 Chain B: C.1, G.2, C.3, T.4, G.5 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.233, D.235 Ligands: XC5.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.233, A:D.235, H2O.3

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

NA.4: 4 residues within 4Å: Chain A: T.143, V.145, V.148 Ligands: DT-DG-DT-DT-DT-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.147, A:V.148, A:V.148

1 x XC5: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine(Non-covalent)

XC5.5: 17 residues within 4Å: Chain A: G.222, G.223, R.226, K.228, G.231, H.232, D.233, D.235, G.340, W.341, T.342, G.343, R.345, E.348 Chain B: G.6 Ligands: DT-DG-DT-DT-DT-DG.1, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.223, A:R.226, A:R.226, A:H.232, A:D.233, A:D.233, A:R.345 Water bridges: A:F.224, A:F.224, A:R.294 Salt bridges: A:K.228, 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
B

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

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