SMTL ID : 7m44.1

DNA Polymerase Lambda, TTP:At Mg2+ Reaction State Ternary Complex, 90 sec

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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: 34 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, G.175, R.179, D.186, D.188, L.228, 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: TTP.3, MG.4, MG.5, NA.6, PPV.9 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.8 Protein-ligand interaction information (PLIP) not available

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

TTP.3: 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-DT.1, DC-DA-DG-DT-DA-DC-DT.1, MG.4, MG.5, PPV.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.264 Hydrogen bonds: A:S.176, A:S.176, A:R.179, A:G.185, A:D.186, A:N.267 Water bridges: A:R.179, A:R.179, A:D.186 Salt bridges: A:R.145, A:R.179

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: D.186, D.188 Ligands: DC-DA-DG-DT-DA-DC-DT.1, TTP.3, MG.5, PPV.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.1 MG.5: 7 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: DC-DA-DG-DT-DA-DC-DT.1, DC-DA-DG-DT-DA-DC-DT.1, TTP.3, MG.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, A:D.244, H2O.8

3 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-DT.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.102, A:A.103, A:A.103 NA.7: 2 residues within 4Å: Chain A: D.121, Q.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.125, A:Q.125 NA.8: 6 residues within 4Å: Chain A: C.59, I.61, P.62, G.63, I.64 Ligands: DG-DC-DC-DG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.63, A:I.64, A:I.64

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.9: 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-DT.1, TTP.3, MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:G.185, A:D.186, A:D.188 Water bridges: A:R.179, A:R.179 Salt bridges: A:R.145, A:R.179

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

EDO.10: 3 residues within 4Å: Chain A: A.133, I.134, K.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.137, A:K.137 Water bridges: A:I.134 EDO.11: 4 residues within 4Å: Chain A: R.123, L.128, A.133, L.136 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.133 EDO.12: 4 residues within 4Å: Chain A: Y.112, Q.113, G.115, R.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.113, A:R.117 EDO.13: 3 residues within 4Å: Chain A: E.89, Y.112, R.117 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.112, A:R.117 Water bridges: A:E.89, A:Y.112 EDO.14: 4 residues within 4Å: Chain A: N.99, W.101, F.142, L.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.99 Water bridges: A:W.101, A:F.142 EDO.15: 5 residues within 4Å: Chain A: F.253, L.257, P.308, T.309, E.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.310 Water bridges: A:E.310, A:K.311

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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