SMTL ID : 8vzl.1

DNA Ligase 1 captured with pre-step 3 ligation at the rG:C nicksite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

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

DG-DT-DC-DG-DG-DA-DC.1: 23 residues within 4Å: Chain A: S.43, A.44, K.484, K.486, Y.489, K.510, T.538, G.539, F.540, S.541, D.542, F.612, R.614 Chain B: G.11 Chain C: G.1, T.2, C.3, C.4, G.5, A.6, C.7, C.8 Ligands: AMP.2 43 PLIP interactions: 43 interactions with chain A Hydrogen bonds: A:R.45, A:R.45, A:R.189, A:L.192, A:G.193, A:L.194, A:A.195, A:E.196, A:Q.197, A:Q.197, A:S.198, A:Q.376, A:S.479, A:S.479, A:R.508, A:R.508, A:K.510, A:K.510, A:K.510, A:K.535, A:S.590, A:S.590, A:Y.595, A:S.609 Water bridges: A:R.189, A:R.383, A:R.383, A:S.479, A:K.510, A:G.516, A:K.535, A:K.535, A:K.535, A:K.535, A:G.537, A:T.538, A:T.538, A:T.538 Salt bridges: A:R.191, A:R.478, A:K.510, A:K.535, A:K.535

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 14 residues within 4Å: Chain A: E.306, Y.307, K.308, Y.309, R.313, E.361, F.400, M.463, K.465, W.482, K.484, K.486 Chain B: G.11 Ligands: DG-DT-DC-DG-DG-DA-DC.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.306, A:E.306, A:K.308, A:Y.309, A:R.313, A:K.465 Water bridges: A:K.484 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

Balu, K.E. et al., Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA. J.Biol.Chem. (2024)

Release Date

2024-05-22

Peptides

DNA ligase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase 1

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