SMTL ID : 6vnp.4 (3 other biounits)

Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

monomer

Ligands

1 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.1: 18 residues within 4Å: Chain A: T.14 Chain B: T.5, A.6 Chain C: D.7, F.8, D.9, Y.10, F.11, Y.12, A.44, T.45, Y.48, R.51, I.104, D.105, K.159 Ligands: MG.2, MG.3 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Y.12 Hydrogen bonds: C:D.9, C:D.9, C:Y.10, C:F.11, C:Y.12, C:T.45, C:T.45, C:Y.48, C:R.51 Water bridges: C:D.7, C:R.51, 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 C: D.7, F.8, D.105, K.159 Ligands: DZ4.1, MG.3 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.7, C:F.8, C:D.105 MG.3: 7 residues within 4Å: Chain A: T.14 Chain C: D.7, S.103, D.105, E.106 Ligands: DZ4.1, MG.2 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.7, C:D.105, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jung, H. et al., Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT. To Be Published

Release Date

2021-02-03

Peptides

DNA polymerase IV: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
J

DNA polymerase IV

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