SMTL ID : 7sx5.1

Crystal structure of ligase I with nick duplexes containing mismatch A:C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG- DA- DC: DNA chain 2(Non-covalent)

DG-DT-DC-DG-DG-DA-DC.1: 20 residues within 4Å: Chain A: S.43, A.44, R.329, K.484, K.486, T.538, G.539, F.540, S.541, D.542, F.612, R.614 Chain C: G.1, T.2, C.3, C.4, G.5, A.6, C.7 Ligands: AMP.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.45, A:R.45, A:G.193, A:A.195, A:Q.197, A:Q.197, A:S.198, A:Q.376, A:R.383, A:K.535, A:T.538, A:S.590, A:Y.595, A:S.609, A:S.609 Water bridges: A:R.191 Salt bridges: A:R.189, A:R.478, A:R.508, A:K.535

1 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.2: 16 residues within 4Å: Chain A: E.306, Y.307, K.308, Y.309, R.313, R.329, E.361, F.400, E.460, M.463, K.465, W.482, K.484, K.486 Ligands: DG-DT-DC-DG-DG-DA-DC.1, DG-DT-DC-DG-DG-DA-DC.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.306, A:Y.309, A:R.313 Salt bridges: A:K.308, A:K.484, A:K.486 pi-Stacking: A:F.400

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, Q. et al., Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair. Nat Commun (2022)

Release Date

2022-07-13

Peptides

DNA ligase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase 1

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