SMTL ID : 6q4u.1

KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

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

MG.1: 7 residues within 4Å: Chain A: D.319, D.494, E.495, K.540 Chain B: C.12 Ligands: MN.2, HHZ.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 MG.5: 4 residues within 4Å: Chain B: C.6, G.7, G.8 Chain C: C.9 No protein-ligand interaction detected (PLIP)

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

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

1 x HHZ: [[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

HHZ.3: 23 residues within 4Å: Chain A: R.282, R.296, D.319, Y.320, S.321, Q.322, I.323, E.324, H.348, R.368, R.369, A.370, K.372, T.373, F.376, Y.380, H.493, D.494 Chain B: C.12 Chain C: T.4, G.5 Ligands: MG.1, MN.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:E.324, A:K.372, A:F.376 Hydrogen bonds: A:R.282, A:D.319, A:S.321, A:Q.322, A:I.323, A:E.324, A:R.369, A:R.369 Water bridges: A:R.282, A:R.296, A:D.319, A:R.369, A:K.372, A:K.372 Salt bridges: A:H.348, A:R.368, A:K.372, A:K.372, A:K.372 pi-Stacking: A:F.376

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

EDO.4: 9 residues within 4Å: Chain A: T.253, Y.254, L.258, P.288, N.289, L.290, N.292, I.293 Chain C: C.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.289 EDO.7: 7 residues within 4Å: Chain B: A.2, C.3, C.4 Chain C: T.12, G.13, G.14, T.15 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain B: C.9 Chain C: T.6, G.7, G.8 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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