SMTL ID : 7m0a.1

Incomplete in crystallo incorporation by DNA Polymerase Lambda bound to blunt-ended DSB substrate and incoming dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

monomer

Ligands

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

DC-DG-DG-DC-DA.1: 14 residues within 4Å: Chain A: W.45, L.48, R.285, R.288, A.289, K.292 Ligands: DC-DA-DG-DT-DG-DC-DT.2, DC-DA-DG-DT-DG-DC-DT.2, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DC-DG.3, DG-DC-DA-DC-DT-DG.4, TTP.5 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.2: 36 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, L.245, R.259, D.261, Y.276, F.277, T.278, G.279, S.280, A.281, N.284 Ligands: DC-DG-DG-DC-DA.1, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4, DG-DC-DA-DC-DT-DG.4, TTP.5, PPV.6, MG.7, CA.8, MG.9, NA.10 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.3: 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.1, DC-DG-DG-DC-DA.1, DC-DG-DG-DC-DA.1, DC-DG-DG-DC-DA.1, NA.11 Protein-ligand interaction information (PLIP) not available

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

DG-DC-DA-DC-DT-DG.4: 19 residues within 4Å: Chain A: V.233, Q.235, Q.241, Q.242, K.243, Y.276, R.288, S.297, L.298, S.299, E.300, H.301 Ligands: DC-DG-DG-DC-DA.1, DC-DA-DG-DT-DG-DC-DT.2, DC-DA-DG-DT-DG-DC-DT.2, DC-DA-DG-DT-DG-DC-DT.2, DC-DA-DG-DT-DG-DC-DT.2, DC-DA-DG-DT-DG-DC-DT.2, DC-DA-DG-DT-DG-DC-DT.2 Protein-ligand interaction information (PLIP) not available

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.5: 23 residues within 4Å: Chain A: R.157, G.187, S.188, R.191, C.196, G.197, D.198, D.200, Y.276, F.277, T.278, G.279, S.280, A.281, N.284 Ligands: DC-DG-DG-DC-DA.1, DC-DA-DG-DT-DG-DC-DT.2, DC-DA-DG-DT-DG-DC-DT.2, PPV.6, MG.7, CA.8, MG.9, NA.12 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.281 Hydrogen bonds: A:S.188, A:S.188, A:S.188, A:R.191, A:G.197, A:D.198, A:N.284 Water bridges: A:R.157, A:R.191, A:R.191, A:R.191, A:D.198, A:R.285 Salt bridges: A:R.157, A:R.191

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.6: 12 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.2, TTP.5, MG.9, NA.12 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.188, A:S.188, A:G.197, A:D.198 Water bridges: A:R.157, A:R.191, A:R.191, A:R.191, A:D.198 Salt bridges: A:R.157, A:R.191

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 8 residues within 4Å: Chain A: D.198, D.200, D.261 Ligands: DC-DA-DG-DT-DG-DC-DT.2, DC-DA-DG-DT-DG-DC-DT.2, TTP.5, CA.8, MG.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.198, A:D.200, A:D.261, H2O.1 MG.9: 7 residues within 4Å: Chain A: D.198, D.200 Ligands: DC-DA-DG-DT-DG-DC-DT.2, TTP.5, PPV.6, MG.7, CA.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.198, A:D.200, H2O.4

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 8 residues within 4Å: Chain A: D.198, D.200, D.261 Ligands: DC-DA-DG-DT-DG-DC-DT.2, DC-DA-DG-DT-DG-DC-DT.2, TTP.5, MG.7, MG.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.198, A:D.200, A:D.261, H2O.1

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

NA.10: 5 residues within 4Å: Chain A: S.110, I.112, G.114, A.115 Ligands: DC-DA-DG-DT-DG-DC-DT.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.112, A:G.114, A:A.115 NA.11: 5 residues within 4Å: Chain A: C.71, I.73, P.74, I.76 Ligands: DG-DC-DC-DG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.73, A:I.76 NA.12: 2 residues within 4Å: Ligands: TTP.5, PPV.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.157

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

CL.13: 3 residues within 4Å: Chain A: Q.41, I.99, S.100 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: N.178, S.179 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: T.326, E.327 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 5 residues within 4Å: Chain A: R.223, L.228, T.229, D.230, D.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.223, A:D.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaminski, A.M. et al., Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining. Nat Commun (2022)

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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