SMTL ID : 6vg6.1 (1 other biounit)

Crystal structure of DPO4 with 8-oxoadenine (oxoA) and dGTP*

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

monomer

Ligands

1 x XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.1: 18 residues within 4Å: Chain A: C.13 Chain B: A.5, G.6 Chain C: D.7, F.8, Y.10, F.11, Y.12, A.44, T.45, Y.48, R.51, M.76, D.105, E.106, K.159 Ligands: MG.2, MG.4 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.12 Hydrogen bonds: C:Y.10, C:F.11, C:Y.12, C:T.45, C:T.45, C:Y.48, C:R.51 Salt bridges: C:R.51, C:K.159

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: C.13 Chain C: D.7, S.103, D.105, E.106 Ligands: XG4.1 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.105, C:E.106 MG.4: 4 residues within 4Å: Chain C: D.7, F.8, D.105 Ligands: XG4.1 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.7, C:F.8, C:D.105

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: T.12 Chain C: D.156, A.181, D.182, V.183, I.186 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.156, C:I.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jung, H. et al., Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4. Biochem.J. (2020)

Release Date

2021-01-06

Peptides

DNA polymerase IV: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase IV

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