SMTL ID : 6dsx.1

Bst DNA polymerase I post-chemistry (n+1 with dATP soak) structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain C: Y.358, S.359, Q.360, D.569 Ligands: MG.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.360, C:Q.360, C:D.569 Water bridges: C:S.359, C:S.359, C:I.361 SO4.2: 3 residues within 4Å: Chain C: R.176, L.177, E.180 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.176, C:R.176 SO4.3: 3 residues within 4Å: Chain C: R.10, T.12, E.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.13 Water bridges: C:E.14 Salt bridges: C:R.10 SO4.4: 4 residues within 4Å: Chain C: L.16, A.17, D.18, H.45 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.18, C:D.18 Salt bridges: C:H.45 SO4.5: 3 residues within 4Å: Chain C: R.127, P.128, A.131 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.127 SO4.6: 3 residues within 4Å: Chain C: H.386, R.406, K.410 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.406, C:K.410 SO4.7: 1 residues within 4Å: Chain C: R.523 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.523, C:R.523 Salt bridges: C:R.523 SO4.8: 1 residues within 4Å: Chain C: R.47 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.47

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain C: D.357, Y.358, D.534 Ligands: SO4.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.534

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chim, N. et al., Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway. Elife (2018)

Release Date

2018-10-31

Peptides

DNA polymerase I: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase I

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