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

D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease) H451 proof-reading deficient variant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: D.216, H.218, D.260, H.418 Ligands: ZN.2, CAC.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.216, A:H.218, A:D.260, A:H.418

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: D.216, D.260, N.306, H.353, H.416 Ligands: FE.1, CAC.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.260, A:H.353, A:H.416

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 7 residues within 4Å: Chain A: I.314, N.338, A.352, H.353, G.354, R.355, L.403 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.403 Hydrogen bonds: A:N.338, A:H.353, A:G.354, A:R.355 Water bridges: A:G.356

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.4: 8 residues within 4Å: Chain A: D.216, H.218, D.260, N.306, H.416, H.418 Ligands: FE.1, ZN.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raia, P. et al., Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases. PLoS Biol. (2019)

Release Date

2019-01-30

Peptides

DNA polymerase II small subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase II small subunit

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