SMTL ID : 5ihe.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.1: 15 residues within 4Å: Chain A: D.216, H.218, D.260, N.306, H.307, E.358, K.392, H.416, V.417, H.418, F.442, V.446, I.448 Ligands: FE.2, ZN.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.306, A:E.358, A:K.392, A:V.417 Salt bridges: A:H.218, A:H.307, A:H.416, A:H.418

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

FE.2: 7 residues within 4Å: Chain A: D.216, H.218, D.260, H.416, H.418 Ligands: D5M.1, ZN.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.216, A:H.218, A:D.260, A:H.418, D5M.1

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: D.216, D.260, N.306, H.353, H.416 Ligands: D5M.1, FE.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.260, A:H.353, A:H.416, D5M.1

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: K.444 No protein-ligand interaction detected (PLIP) CA.6: 1 residues within 4Å: Chain A: E.241 No protein-ligand interaction detected (PLIP)

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

ACT.5: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauguet, L. et al., Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography. Nat Commun (2016)

Release Date

2016-08-31

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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