SMTL ID : 6fbf.1

KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the fourth primer nucleotide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.319, D.494, E.495 Chain B: C.12 Ligands: MN.2, XG4.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.319, A:D.494, H2O.1, H2O.2 MN.2: 8 residues within 4Å: Chain A: D.319, Y.320, S.321, Q.322, I.323, D.494 Ligands: MN.1, XG4.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.319, A:Y.320, A:D.494

1 x XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.3: 23 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, R.369, K.372, T.373, F.376, Y.380, N.459, H.493, D.494 Chain B: C.12 Chain C: C.4, G.5 Ligands: MN.1, MN.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:E.324, A:F.376 Hydrogen bonds: A:R.282, A:S.321, A:Q.322, A:I.323, A:E.324, A:H.348, A:R.369, A:R.369, A:K.372 Water bridges: A:R.282, A:D.319, A:D.319, A:E.324, A:N.459 Salt bridges: A:R.368, A:K.372 pi-Stacking: A:F.376, A:F.376

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kropp, H.M. et al., Snapshots of a modified nucleotide moving through the confines of a DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-09-26

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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