SMTL ID : 4xus.1

Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating A and an incoming dTTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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: 17 residues within 4Å: Chain A: Y.17, W.24, R.25, G.28, Y.29, P.53, G.54, I.55, G.56, K.57, R.58, M.59, K.62 Chain B: C.1, G.2, G.3, C.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.24, A:L.27 Hydrogen bonds: A:W.24, A:R.267, A:R.288 Salt bridges: A:R.264, A:K.271, A:K.271, A:H.291 pi-Stacking: A:W.24, A:W.24

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

DC-DA-DG-DT-DA.2: 16 residues within 4Å: Chain A: I.91, W.92, G.93, A.94, G.95, T.96, K.97, T.98 Chain B: G.6, T.7, A.8, C.9, T.10, G.11 Ligands: MG.4, DOC.6 Protein-ligand interaction information (PLIP) not available

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

TTP.3: 18 residues within 4Å: Chain A: R.136, G.166, S.167, R.170, C.175, G.176, D.177, D.179, Y.255, F.256, T.257, G.258, S.259, A.260, N.263 Chain B: A.5 Ligands: MG.5, DOC.6 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.260 Hydrogen bonds: A:S.167, A:S.167, A:R.170, A:G.176, A:D.177, A:D.177, A:D.177, A:N.263 Water bridges: A:R.238, A:R.238, A:R.238, A:A.260 Salt bridges: A:R.136, A:R.170

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: S.89, I.91, A.94 Ligands: DC-DA-DG-DT-DA.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.89, A:I.91, A:A.94, H2O.3, H2O.8 MG.5: 3 residues within 4Å: Chain A: D.177, D.179 Ligands: TTP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.177, A:D.179, H2O.3

1 x DOC: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DOC.6: 9 residues within 4Å: Chain A: W.92, L.224, R.238, D.240, Y.255 Chain B: A.5, G.6 Ligands: DC-DA-DG-DT-DA.2, TTP.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.255 Water bridges: A:K.222, A:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burak, M.J. et al., Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda. Nucleic Acids Res. (2015)

Release Date

2016-02-03

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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