SMTL ID : 5iio.1 (3 other biounits)

Crystal structure of the DNA polymerase lambda binary complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC.1: 21 residues within 4Å: Chain A: G.5, G.6, T.7, A.8, C.9, T.10, G.11 Chain B: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, K.231, L.233, R.247, Y.264, F.265 Ligands: NA.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.33 Hydrogen bonds: B:E.225, B:Y.264, B:Y.264 Water bridges: B:W.33, B:S.222, B:E.224, B:E.225, B:N.226, B:G.227, B:E.288 Salt bridges: B:K.280 pi-Stacking: B:W.33

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: C.1, G.2, G.3, C.4 Chain B: 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 Ligands: NA.4 Protein-ligand interaction information (PLIP) not available

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

NA.3: 4 residues within 4Å: Chain B: S.98, I.100, A.103 Ligands: DC-DA-DG-DT-DA-DC.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.100, B:G.102, B:A.103 NA.4: 6 residues within 4Å: Chain B: C.59, I.61, P.62, G.63, I.64 Ligands: DG-DC-DC-DG.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.61, B:G.63, B:I.64

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: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA polymerase lambda

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