SMTL ID : 3au6.1

DNA polymerase X from Thermus thermophilus HB8 ternary complex with primer/template DNA and ddGTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DT-DDG.1: 11 residues within 4Å: Chain A: D.243, Y.258 Chain B: C.5, A.6, T.7, A.8, C.9, T.10, G.11 Ligands: DG3.2, MG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.258

1 x DG3: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DG3.2: 17 residues within 4Å: Chain A: R.157, G.187, S.188, R.191, V.196, G.197, D.198, D.200, Y.258, L.259, G.261, K.263, R.270 Chain B: C.4 Ligands: DC-DA-DG-DT-DA-DT-DDG.1, MG.3, MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.188, A:S.188, A:G.197, A:D.198, A:D.198, A:D.198, A:R.270 Salt bridges: A:R.157, A:R.191

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.188, D.198, D.200 Ligands: DG3.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.188, A:D.200 MG.4: 5 residues within 4Å: Chain A: D.198, D.200, D.243 Ligands: DC-DA-DG-DT-DA-DT-DDG.1, DG3.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.198, A:D.200

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: E.413, H.440, H.468, R.506, D.529 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.413, A:H.468

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 1 residues within 4Å: Chain A: K.193 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: D.426, W.427 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: Q.336, K.338 Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 5 residues within 4Å: Chain A: H.440, F.443, L.473, R.477, R.506 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.440, A:R.477, A:R.506

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakane, S. et al., The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA. J.Mol.Biol. (2012)

Release Date

2012-01-25

Peptides

DNA polymerase beta family (X family): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta family (X family)

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