SMTL ID : 6q4v.1

KlenTaq DNA polymerase in complex with dATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 21 residues within 4Å: Chain A: R.282, D.319, Y.320, S.321, Q.322, I.323, E.324, L.325, H.348, R.368, K.372, T.373, F.376, Y.380, H.493, D.494 Chain B: C.12 Chain C: T.4, G.5 Ligands: MG.2, MN.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:E.324, A:F.376 Hydrogen bonds: A:R.282, A:Q.322, A:I.323, A:E.324 Water bridges: A:R.282, A:Y.320, A:S.321, A:K.372, A:Y.380, A:K.540, A:K.540 Salt bridges: A:H.348, A:R.368, A:K.372, A:K.372, A:K.372 pi-Stacking: A:F.376

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.319, D.494, E.495, K.540 Chain B: C.12 Ligands: DTP.1, MN.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.319, A:D.494, H2O.2, H2O.3

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 6 residues within 4Å: Chain A: D.319, Y.320, I.323, D.494 Ligands: DTP.1, MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.319, A:Y.320, A:D.494

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain B: A.2, C.3 Chain C: T.12, G.13, G.14, T.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kropp, H.M. et al., The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide. Angew.Chem.Int.Ed.Engl. (2019)

Release Date

2019-02-27

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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