SMTL ID : 7m0c.1

Post-catalytic nicked complex of DNA Polymerase Lambda with bound mismatched DSB substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

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

DC-DG-DG-DC-DA-DG.1: 18 residues within 4Å: Chain A: W.45, L.48, Y.276, R.285, R.288, A.289, K.292, L.298, S.299, E.300 Ligands: DT-DA-DC-DT-DG.2, DC-DA-DG-DT-DG-DC-DT.3, DC-DA-DG-DT-DG-DC-DT.3, DC-DA-DG-DT-DG-DC-DT.3, DG-DC-DC-DG.4, DG-DC-DC-DG.4, DG-DC-DC-DG.4, DG-DC-DC-DG.4 Protein-ligand interaction information (PLIP) not available

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

DT-DA-DC-DT-DG.2: 15 residues within 4Å: Chain A: V.233, S.234, Q.235, Q.241, Q.242, K.243, S.299, E.300, H.301 Ligands: DC-DG-DG-DC-DA-DG.1, DC-DA-DG-DT-DG-DC-DT.3, DC-DA-DG-DT-DG-DC-DT.3, DC-DA-DG-DT-DG-DC-DT.3, DC-DA-DG-DT-DG-DC-DT.3, DC-DA-DG-DT-DG-DC-DT.3 Protein-ligand interaction information (PLIP) not available

1 x DC- DA- DG- DT- DG- DC- DT: DNA (5'-D(*CP*AP*GP*TP*GP*CP*T)-3')(Non-covalent)

DC-DA-DG-DT-DG-DC-DT.3: 33 residues within 4Å: Chain A: I.112, W.113, G.114, A.115, G.116, T.117, K.118, T.119, G.187, R.191, D.198, D.200, K.243, R.259, D.261, Y.276, F.277, T.278, G.279, S.280, A.281, N.284 Ligands: DC-DG-DG-DC-DA-DG.1, DC-DG-DG-DC-DA-DG.1, DT-DA-DC-DT-DG.2, DT-DA-DC-DT-DG.2, DT-DA-DC-DT-DG.2, DT-DA-DC-DT-DG.2, DT-DA-DC-DT-DG.2, MG.5, MG.6, NA.7, PPV.11 Protein-ligand interaction information (PLIP) not available

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

DG-DC-DC-DG.4: 19 residues within 4Å: Chain A: Y.38, W.45, R.46, G.49, Y.50, I.73, P.74, G.75, I.76, G.77, K.78, R.79, M.80, K.83 Ligands: DC-DG-DG-DC-DA-DG.1, DC-DG-DG-DC-DA-DG.1, DC-DG-DG-DC-DA-DG.1, DC-DG-DG-DC-DA-DG.1, NA.8 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: D.198, D.200, D.261 Ligands: DC-DA-DG-DT-DG-DC-DT.3, DC-DA-DG-DT-DG-DC-DT.3, MG.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.198, A:D.200, A:D.261 MG.6: 5 residues within 4Å: Chain A: D.198, D.200 Ligands: DC-DA-DG-DT-DG-DC-DT.3, MG.5, PPV.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.198, A:D.200, H2O.2

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

NA.7: 5 residues within 4Å: Chain A: S.110, I.112, W.113, A.115 Ligands: DC-DA-DG-DT-DG-DC-DT.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.114, A:A.115, A:A.115 NA.8: 4 residues within 4Å: Chain A: C.71, I.73, I.76 Ligands: DG-DC-DC-DG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.73

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 1 residues within 4Å: Chain A: S.286 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: T.326, E.327 Ligand excluded by PLIP

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.11: 10 residues within 4Å: Chain A: R.157, G.187, S.188, R.191, C.196, G.197, D.198, D.200 Ligands: DC-DA-DG-DT-DG-DC-DT.3, MG.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.188, A:S.188, A:G.197, A:D.198 Water bridges: A:R.157, A:Y.189, A:Y.189, A:R.191, A:R.191, A:R.191 Salt bridges: A:R.157, A:R.191

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 2 residues within 4Å: Chain A: K.19, K.58 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.19, A:K.58

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 2 residues within 4Å: Chain A: R.249, H.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.249, A:R.249, A:H.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaminski, A.M. et al., Comprehensive structural survey of DNA double-strand break synapsis by DNA Polymerase Lambda. Not Published

Release Date

2022-03-16

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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