SMTL ID : 5w6k.1

Structure of mutant Taq Polymerase incorporating unnatural base pairs Z:P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

monomer

Ligands

1 x A5J: (1R)-1-[6-amino-5-(dihydroxyamino)-2-hydroxypyridin-3-yl]-1,4-anhydro-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-erythro-pentitol(Non-covalent)

A5J.1: 22 residues within 4Å: Chain A: R.281, D.318, Y.319, S.320, Q.321, I.322, E.323, L.324, H.347, R.367, R.368, K.371, T.372, F.375, Y.379, Q.462, D.493 Chain B: C.12 Chain C: X.1, G.2 Ligands: MG.2, MG.3 19 PLIP interactions: 19 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 Water bridges: A:R.281, A:D.318, A:Y.319, A:E.323, 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: D.318, Y.319, S.320, Q.321, I.322, D.493 Ligands: A5J.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MG.3: 6 residues within 4Å: Chain A: D.318, D.493, E.494 Chain B: C.12 Ligands: A5J.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.2, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, I. et al., Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide. Nucleic Acids Res. (2018)

Release Date

2018-07-18

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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