SMTL ID : 6dsu.1

Bst DNA polymerase I pre-insertion complex structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain C: Y.358, S.359, Q.360 Ligands: DZ4.5 No protein-ligand interaction detected (PLIP)

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

SO4.2: 5 residues within 4Å: Chain C: E.371, D.372, D.373, P.448, G.449 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.373, C:D.373, C:G.449 Water bridges: C:N.374 SO4.3: 1 residues within 4Å: Chain C: R.47 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.47 SO4.4: 2 residues within 4Å: Chain C: S.432, R.433 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.433

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

DZ4.5: 14 residues within 4Å: Chain A: T.10 Chain C: R.319, D.357, Y.358, Q.360, E.362, H.386, R.406, K.410, V.417, Y.418, Q.501, D.534 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:R.319, C:D.357, C:Y.358, C:Q.360, C:H.386, C:K.410, C:K.410, C:Y.418, C:Q.501 Water bridges: C:E.362, C:D.534, C:D.534 Salt bridges: C:H.386, C:R.406, C:K.410

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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