SMTL ID : 5edw.1

Ternary structure of Dpo4 bound to G in the template base paired with incoming dTTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.7, F.8, D.105, K.159 Ligands: CA.2, TTP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.7, A:F.8, A:D.105 CA.2: 6 residues within 4Å: Chain A: D.7, D.105, E.106 Chain C: C.13 Ligands: CA.1, TTP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.7, A:D.7, A:E.106 CA.3: 2 residues within 4Å: Chain A: A.181, I.186 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.181, A:I.186, H2O.1, H2O.2

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

TTP.4: 18 residues within 4Å: Chain A: D.7, F.8, D.9, Y.10, F.11, Y.12, A.44, T.45, Y.48, R.51, A.57, D.105, K.159 Chain B: G.6, G.7 Chain C: C.13 Ligands: CA.1, CA.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.12, A:T.45, A:A.57 Hydrogen bonds: A:D.9, A:Y.10, A:F.11, A:Y.12, A:Y.48, A:D.105 Salt bridges: A:R.51, A:R.51, A:K.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.-C. et al., Structure of Dpo4 DNA polymerase replicating across the genotoxic N7-methylguanine lesion. To Be Published

Release Date

2016-11-02

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

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