SMTL ID : 7m4e.1

DNA Polymerase Lambda, dCTP:At Mg2+ Reaction State Ternary Complex, 120 min

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC-DC.1: 32 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, R.179, D.186, D.188, R.242, D.244, Y.259, F.260, T.261, G.262, S.263, A.264, N.267 Chain B: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: PPV.3, MG.4, MG.5, NA.6, DCP.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: 18 residues within 4Å: Chain A: Y.26, W.33, R.34, G.37, Y.38, P.62, G.63, I.64, G.65, K.66, R.67, M.68, K.71 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.7 Protein-ligand interaction information (PLIP) not available

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3: 11 residues within 4Å: Chain A: R.145, G.175, S.176, R.179, C.184, G.185, D.186, D.188 Ligands: DC-DA-DG-DT-DA-DC-DC.1, MG.5, DCP.8 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:S.176, A:G.185, A:D.186, A:D.188 Salt bridges: A:R.145, A:R.179

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: DC-DA-DG-DT-DA-DC-DC.1, DC-DA-DG-DT-DA-DC-DC.1, MG.5, DCP.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, A:D.244, H2O.1 MG.5: 6 residues within 4Å: Chain A: D.186, D.188 Ligands: DC-DA-DG-DT-DA-DC-DC.1, PPV.3, MG.4, DCP.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.1

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

NA.6: 6 residues within 4Å: Chain A: S.98, I.100, W.101, G.102, A.103 Ligands: DC-DA-DG-DT-DA-DC-DC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.100, A:G.102, A:A.103 NA.7: 4 residues within 4Å: Chain A: C.59, I.61, I.64 Ligands: DG-DC-DC-DG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.61

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.8: 21 residues within 4Å: Chain A: R.145, G.175, S.176, R.179, C.184, G.185, D.186, D.188, Y.259, F.260, T.261, G.262, S.263, A.264, N.267 Chain B: A.5 Ligands: DC-DA-DG-DT-DA-DC-DC.1, DC-DA-DG-DT-DA-DC-DC.1, PPV.3, MG.4, MG.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:S.176, A:R.179, A:G.185, A:D.186, A:N.267 Water bridges: A:R.271 Salt bridges: A:R.145, A:R.179

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

EDO.9: 3 residues within 4Å: Chain A: R.117, S.118, D.121 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamsen, J.A. et al., Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints. Nat Commun (2022)

Release Date

2022-07-06

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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