SMTL ID : 8sck.1 (1 other biounit)

Bst DNA polymerase I Large Fragment mutant F710Y/D598A with 3'-amino primer, dGTP, and calcium time-resolved 4h

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.1: 11 residues within 4Å: Chain A: Y.357, S.358, Q.359, H.385, R.405, K.409, Y.413, D.533 Chain B: G.10 Ligands: DGT.2, CA.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.357, A:Q.359, A:Y.413, A:D.533 Water bridges: A:I.360 Salt bridges: A:H.385, A:R.405, A:K.409, A:K.409

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.2: 19 residues within 4Å: Chain A: R.318, Y.357, S.358, Q.359, E.361, H.385, R.405, K.409, A.410, Y.413, Y.417, N.496, D.533 Chain B: C.9, G.10 Chain C: C.3, G.4 Ligands: DPO.1, CA.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.318, A:Q.359, A:Y.413, A:N.496, A:D.533 Water bridges: A:K.409 Salt bridges: A:H.385, A:R.405, A:K.409, A:K.409, A:K.409 pi-Stacking: A:Y.413, A:Y.413

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.356, Y.357, D.533 Chain B: G.10 Ligands: DPO.1, DGT.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.356, A:Y.357, A:D.533

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

SO4.4: 2 residues within 4Å: Chain A: L.295, P.300 No protein-ligand interaction detected (PLIP) SO4.5: 4 residues within 4Å: Chain A: K.1, M.2, A.3, R.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.3 Salt bridges: A:R.46 SO4.6: 1 residues within 4Å: Chain A: V.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.249 SO4.7: 2 residues within 4Å: Chain A: N.373, R.380 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lelyveld, V.S. et al., Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity. Science (2023)

Release Date

2023-10-25

Peptides

DNA polymerase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I

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