SMTL ID : 9fmf.1

KlenTaq DNA polymerase in a ternary complex with primer/template and a fluorobenzofuran-modified dUTP (FBFdUTP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: 01.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493

1 x 01: [[(2~{R},3~{S},5~{R})-5-[5-(5-fluoranyl-1-benzofuran-2-yl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

01.2: 19 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, D.493 Chain B: C.12 Chain C: A.4, G.5 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.323, A:K.371, A:T.372, A:F.375 Hydrogen bonds: A:R.281, A:Y.319, A:Q.321, A:I.322, A:E.323 Water bridges: A:K.371, A:K.371 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: T.252, Y.253, P.256, P.287, N.288, N.291 Chain C: C.9, C.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.288, A:N.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, P. et al., Structures of a DNA Polymerase Caught while Incorporating Responsive Dual-Functional Nucleotide Probes. Angew.Chem.Int.Ed.Engl. (2024)

Release Date

2024-11-13

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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