SMTL ID : 7owf.1

KlenTaq DNA polymerase in a ternary complex with primer/template and the fluorescent nucleotide analog BFdUTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 8 residues within 4Å: Chain A: D.318, Y.319, S.320, Q.321, I.322, D.493 Ligands: MG.2, 2IU.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MG.2: 6 residues within 4Å: Chain A: D.318, D.493, E.494 Chain B: C.12 Ligands: MG.1, 2IU.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.1, H2O.2 MG.5: 2 residues within 4Å: Chain B: G.1, A.2 No protein-ligand interaction detected (PLIP)

1 x 2IU: [[(2R,3S,5R)-5-[5-(1-benzofuran-2-yl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

2IU.3: 21 residues within 4Å: Chain A: R.281, R.295, D.318, Y.319, S.320, Q.321, I.322, E.323, H.347, R.367, R.368, K.371, T.372, F.375, Y.379, D.493 Chain B: C.12 Chain C: A.4, G.5 Ligands: MG.1, MG.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:E.323, A:R.368, A:K.371, A:F.375 Hydrogen bonds: A:R.281, A:S.320, A:Q.321, A:I.322, A:E.323 Water bridges: A:K.371, A:K.371, A:Y.379 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375 pi-Cation interactions: A:K.371

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain B: C.6, G.7, G.8 Chain C: C.9, C.10 Ligands: GOL.6 No protein-ligand interaction detected (PLIP) GOL.6: 6 residues within 4Å: Chain B: C.9 Chain C: T.6, G.7, G.8, C.9 Ligands: GOL.4 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain B: A.2, C.3 Chain C: T.12, G.13, G.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, P. et al., Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases. J.Am.Chem.Soc. (2022)

Release Date

2022-06-29

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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