SMTL ID : 9fm3.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

monomer

Ligands

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

01.1: 19 residues within 4Å: Chain A: R.281, 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 C: A.4, G.5 Ligands: MG.2, DOC.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.323, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:I.322, A:E.323, A:D.493 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 MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: 01.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493

1 x DOC: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DOC.3: 11 residues within 4Å: Chain A: R.281, V.294, R.303, R.368, V.491, H.492, D.493 Chain B: A.11 Chain C: G.5, T.6 Ligands: 01.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.281, A:R.281, A:H.492 Water bridges: A:R.303, A:E.494, A:K.539, A:K.539 Salt bridges: A:R.303, A:R.368

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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