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

Bst DNA polymerase I Large Fragment wildtype D598A with 3'-amino primer, dGTP, and calcium time-resolved 2h

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.1: 13 residues within 4Å: Chain A: D.356, Y.357, S.358, Q.359, I.360, H.385, R.405, K.409, F.413, D.533 Chain B: G.10 Ligands: DGT.2, CA.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.356, A:Y.357, A:Q.359, 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, D.356, Y.357, S.358, Q.359, I.360, E.361, H.385, R.405, K.409, F.413, Y.417, D.533 Chain B: C.9, G.10 Chain C: C.3, G.4 Ligands: DPO.1, CA.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.361, A:F.413 Hydrogen bonds: A:R.318, A:Q.359, A:I.360, A:E.361, A:N.496 Salt bridges: A:H.385, A:R.405, A:K.409, A:K.409, A:K.409 pi-Stacking: A:F.413, A:F.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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.356, A:D.356, A:Y.357, A:D.533

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

SO4.4: 4 residues within 4Å: Chain A: N.373, R.380, L.382 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.373 Salt bridges: A:R.380 SO4.5: 2 residues within 4Å: Chain A: R.380 Ligands: SO4.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.380 SO4.6: 4 residues within 4Å: Chain A: R.9, V.10, T.11, E.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.12 Salt bridges: A:R.9 SO4.7: 2 residues within 4Å: Chain A: E.204, P.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.204 Water bridges: A:E.204, A:V.298 SO4.8: 4 residues within 4Å: Chain A: A.16, D.17, E.43, H.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.17 Salt bridges: A:H.44 SO4.9: 4 residues within 4Å: Chain A: E.27, E.28, N.29, R.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.28, A:N.29, A:R.138 SO4.10: 2 residues within 4Å: Chain A: R.482, N.483 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.483 Salt bridges: A:R.482 SO4.11: 1 residues within 4Å: Chain A: R.379 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.379 SO4.12: 3 residues within 4Å: Chain B: G.1, C.2 Chain C: C.10 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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