SMTL ID : 7m4j.1

DNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex, 960 min

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 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: 31 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: MN.3, NA.5, NA.7, PO4.8 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: 20 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, K.83 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.6 Protein-ligand interaction information (PLIP) not available

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 5 residues within 4Å: Chain A: D.186, D.188 Ligands: DC-DA-DG-DT-DA-DC-DC.1, NA.7, PO4.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.186, A:D.188 MN.4: 2 residues within 4Å: Chain A: D.141, H.240 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.141, A:H.240, H2O.1, H2O.2, H2O.2

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

NA.5: 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:G.102, A:A.103, A:A.103 NA.6: 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 NA.7: 6 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, MN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.244

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 5 residues within 4Å: Chain A: S.176, G.185, D.186 Ligands: DC-DA-DG-DT-DA-DC-DC.1, MN.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.176, A:G.185, A:D.186, A:D.186

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

EDO.9: 3 residues within 4Å: Chain A: R.123, L.128, A.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.123 EDO.10: 3 residues within 4Å: Chain A: N.99, W.101, F.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.99 Water bridges: A:W.101, A:F.142 EDO.11: 4 residues within 4Å: Chain A: L.257, P.308, T.309, E.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.310 EDO.12: 1 residues within 4Å: Chain A: Q.125 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.125, A:Q.125, A:Q.125

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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