SMTL ID : 4xa5.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x DG- DC- DC- DG: DOWNSTREAM PRIMER 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, I.52, P.53, G.54, I.55, G.56, R.58, M.59, K.62 Chain B: C.1, G.2, G.3, C.4 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:W.24 Hydrogen bonds: A:W.24, A:T.121, A:S.213, A:S.213, A:Q.214, A:Q.221, A:Q.221, A:K.222, A:K.222, A:R.267 Water bridges: A:T.121, A:T.121, A:Q.122, A:Q.122, A:N.217, A:Y.255, A:R.264, A:K.271, A:K.271, A:S.278, A:E.279 Salt bridges: A:R.264, A:K.271, A:K.271, A:E.279, A:H.280 pi-Stacking: A:W.24, A:W.24

1 x DC- DA- DG- DT- DA- DOC: PRIMER 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.91, W.92, G.93, A.94, G.95, T.96, K.97, T.98, R.238, D.240, Y.255 Chain B: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: 8DG.3, MG.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.255 Water bridges: A:K.222, A:R.238, A:R.238, A:E.279 Salt bridges: A:R.238

1 x 8DG: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

8DG.3: 17 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, A.260, N.263 Chain B: A.5 Ligands: DC-DA-DG-DT-DA-DOC.2, MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.167, A:S.167, A:R.170, A:G.176, A:D.177, A:D.177, A:N.263 Water bridges: A:G.176, A:D.177, A:A.260 Salt bridges: A:R.136, A:R.170

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.177, D.179 Ligands: 8DG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.177, A:D.179, H2O.3 MG.5: 6 residues within 4Å: Chain A: S.89, I.91, W.92, G.93, A.94 Ligands: DC-DA-DG-DT-DA-DOC.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

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 2 residues within 4Å: Chain A: R.139, Y.168 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.139, A:T.143 Salt bridges: A:R.139 ACT.7: 8 residues within 4Å: Chain A: H.190, G.192, I.193, F.194, G.218, Q.219, Q.220, V.243 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.194 Hydrogen bonds: A:G.192, A:G.218 ACT.8: 4 residues within 4Å: Chain A: Y.17, Q.20, I.78, S.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.20, A:S.79

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: R.202, L.207, T.208, D.209, D.210 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.202, A:R.202, A:D.210 Water bridges: A:T.208 GOL.10: 5 residues within 4Å: Chain A: Q.221, V.243, V.244, P.245, H.280 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.248

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

2016-02-10

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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