SMTL ID : 5yux.2 (1 other biounit)

DNA polymerase IV - DNA ternary complex 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

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

TTP.1: 20 residues within 4Å: Chain A: D.9, M.10, D.11, C.12, F.13, F.14, S.43, T.44, R.50, S.56, D.104, E.105, K.158 Chain B: A.4, G.5 Chain C: C.18, T.19 Ligands: MG.2, MG.3, DPO.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.14, A:T.44 Hydrogen bonds: A:C.12, A:F.13, A:F.14 Water bridges: A:D.9, A:D.9, A:S.43 Salt bridges: A:R.50, A:R.50, A:K.158, A:K.158

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: D.9, M.10, D.104, K.158 Chain C: T.19 Ligands: TTP.1, MG.3, DPO.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.9, A:M.10, A:D.104 MG.3: 7 residues within 4Å: Chain A: D.9, D.104, E.105 Chain C: C.18, T.19 Ligands: TTP.1, MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.9, A:D.104, A:E.105

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.4: 11 residues within 4Å: Chain A: M.10, D.11, C.12, F.13, T.44, R.50, D.104, K.158 Chain C: T.19 Ligands: TTP.1, MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:C.12, A:F.13, A:T.44, A:D.104 Salt bridges: A:R.50, A:R.50, A:K.158, A:K.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kottur, J. et al., Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction. Nucleic Acids Res. (2018)

Release Date

2018-12-19

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

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