SMTL ID : 6fbc.1

KlenTaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

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

XG4.1: 22 residues within 4Å: Chain A: R.282, D.319, Y.320, S.321, Q.322, I.323, E.324, 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.3, MN.4 22 PLIP interactions: 22 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, A:H.348, A:R.369, A:K.372 Water bridges: A:R.282, A:E.324, A:R.368, A:R.368, A:R.368, A:R.368, A:R.369, A:T.373, A:N.459, A:K.540 Salt bridges: A:R.368 pi-Stacking: A:F.376, A:F.376

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

EDO.2: 7 residues within 4Å: Chain A: E.180, F.184, F.191, N.192, L.193, N.194, Y.244 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.180, A:E.180, A:N.192, A:L.193, A:N.194 EDO.7: 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)

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

MN.3: 7 residues within 4Å: Chain A: D.319, D.494, E.495, K.540 Chain B: C.12 Ligands: XG4.1, MN.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.319, A:D.494, H2O.1, H2O.5 MN.4: 7 residues within 4Å: Chain A: D.319, Y.320, Q.322, I.323, D.494 Ligands: XG4.1, MN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.319, A:Y.320, A:D.494

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

MG.5: 2 residues within 4Å: Chain A: E.171, R.302 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.171, H2O.4, H2O.7 MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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