SMTL ID : 3khr.2 (1 other biounit)

Dpo4 post-extension ternary complex with the correct C opposite the 2-aminofluorene-guanine [AF]G lesion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

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

TTP.1: 17 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.13 Chain C: A.4 Ligands: CA.2, CA.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.12, A:A.57 Hydrogen bonds: A:F.8, A:Y.10, A:F.11, A:Y.12, A:T.45 Water bridges: A:D.9 Salt bridges: A:R.51, A:R.51, A:K.159, A:K.159

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.7, E.106, K.152 Chain B: G.13 Ligands: TTP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.7, A:E.106 CA.3: 4 residues within 4Å: Chain A: D.7, F.8, D.105 Ligands: TTP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.7, A:F.8, A:D.105, H2O.6 CA.4: 2 residues within 4Å: Chain A: A.181, I.186 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.181, A:I.186, H2O.5, H2O.6, H2O.7

1 x AF: 2-AMINOFLUORENE(Non-covalent)

AF.5: 9 residues within 4Å: Chain A: R.247, I.248, H.285, V.287, V.335, R.336 Chain C: C.5, G.6, C.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.248, A:I.248, A:V.287, A:V.287, A:R.336 Water bridges: A:R.332 pi-Cation interactions: A:R.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rechkoblit, O. et al., Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-02-16

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA polymerase IV

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