SMTL ID : 7m4b.1

DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 60 min

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 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: MN.3, MN.4, NA.6, PPV.9, MN.15 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.26, W.33, R.34, G.37, Y.38, I.61, 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

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.3: 5 residues within 4Å: Chain A: D.186, D.188 Ligands: DC-DA-DG-DT-DA-DC-DT.1, MN.4, PPV.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.2 MN.4: 6 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, MN.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, A:D.244, H2O.1, H2O.6 MN.5: 3 residues within 4Å: Chain A: D.141, R.239, H.240 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.141, A:H.240, H2O.3, H2O.4, H2O.6 MN.15: 2 residues within 4Å: Ligands: DC-DA-DG-DT-DA-DC-DT.1, PPV.9 No protein-ligand interaction detected (PLIP)

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: 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:I.61, A:G.63, A:I.64 NA.8: 1 residues within 4Å: Chain A: Q.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.125, A:Q.125

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, MN.3, MN.15 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:S.176, A:G.185, A:D.186 Salt bridges: A:R.145, A:R.179

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

EDO.10: 1 residues within 4Å: Chain A: Y.112 No protein-ligand interaction detected (PLIP) 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: 5 residues within 4Å: Chain A: R.178, L.257, P.308, T.309, E.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.178, A:P.308, A:E.310 Water bridges: A:E.310 EDO.13: 4 residues within 4Å: Chain A: N.99, W.101, F.142, L.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.99 Water bridges: A:W.101 EDO.14: 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 Water bridges: A:T.130, A:I.134

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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