SMTL ID : 5iij.1

Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dG and an incoming dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

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

DG-DC-DC-DG.1: 18 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.33 Hydrogen bonds: A:R.276 Water bridges: A:W.33 Salt bridges: A:K.280, A:K.280 pi-Stacking: A:W.33

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

DC-DA-DG-DT-DA-DOC.2: 20 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, R.247, D.249, Y.264 Chain B: G.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: DCT.3, NA.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.247, A:R.247 Salt bridges: A:R.247

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.3: 17 residues within 4Å: Chain A: R.145, G.175, S.176, R.179, C.184, G.185, D.186, D.188, Y.264, F.265, G.267, A.269, N.272, R.273 Chain B: G.5 Ligands: DC-DA-DG-DT-DA-DOC.2, MG.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.269 Hydrogen bonds: A:S.176, A:S.176, A:S.176, A:G.185, A:D.186, A:N.272, A:R.273 Water bridges: A:R.179, A:R.179 Salt bridges: A:R.145, A:R.179

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.186, D.188 Ligands: DCT.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.4

2 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-DOC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.102, A:A.103, A:A.103 NA.6: 2 residues within 4Å: Chain A: S.222 Chain B: T.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burak, M.J. et al., A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG. Embo J. (2016)

Release Date

2016-08-17

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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