SMTL ID : 5o7t.1

Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a dG:dCTP base pair

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

MG.1: 6 residues within 4Å: Chain A: D.318, Y.319, I.322, D.493 Ligands: MG.2, DCP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MG.2: 7 residues within 4Å: Chain A: D.318, D.493, E.494, K.539 Chain B: G.12 Ligands: MG.1, DCP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.2, H2O.6 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.3: 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, K.371, T.372, F.375, Y.379, H.492, D.493 Chain B: G.12 Chain C: G.4, C.5 Ligands: MG.1, MG.2, GOL.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:E.323, A:F.375 Hydrogen bonds: A:R.281, A:Y.319, A:Q.321, A:I.322, A:E.323, A:T.372 Water bridges: A:R.281, A:R.367, A:R.367, A:K.371, A:K.371, A:Y.379, A:K.539, A:K.539 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.5: 8 residues within 4Å: Chain A: T.372, R.385 Chain B: C.11, G.12 Chain C: G.4, C.5, G.6 Ligands: DCP.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.372, A:T.372, A:R.385 Water bridges: A:R.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Betz, K. et al., Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase. Chem. Commun. (Camb.) (2017)

Release Date

2017-11-29

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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