SMTL ID : 7m08.1

Post-catalytic nicked complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC-DT.1: 31 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, L.245, R.259, D.261, Y.276, F.277, T.278, G.279, S.280, A.281, N.284 Chain B: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: NA.3, MG.8 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.2: 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 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.4 Protein-ligand interaction information (PLIP) not available

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

NA.3: 5 residues within 4Å: Chain A: S.110, I.112, W.113, A.115 Ligands: DC-DA-DG-DT-DA-DC-DT.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.112, A:G.114, A:A.115 NA.4: 4 residues within 4Å: Chain A: C.71, I.73, I.76 Ligands: DG-DC-DC-DG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.76 NA.5: 5 residues within 4Å: Chain A: Q.18, T.21, K.58, S.59, F.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.58 Water bridges: A:H.23

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

CL.6: 2 residues within 4Å: Chain A: T.326, E.327 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: R.288, E.300 Chain B: G.6, T.7 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 5 residues within 4Å: Chain A: D.198, D.200, D.261 Ligands: DC-DA-DG-DT-DA-DC-DT.1, DC-DA-DG-DT-DA-DC-DT.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.198, A:D.198, A:D.200, A:D.261

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

EDO.9: 4 residues within 4Å: Chain A: R.157, S.188, R.191, G.197 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.157, A:R.157, A:S.188, A:R.191, A:G.197 Water bridges: A:S.188, A:S.188

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 4 residues within 4Å: Chain A: A.176, F.177, N.178, S.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.179

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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