SMTL ID : 3rr8.1

Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x DG3: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DG3.1: 9 residues within 4Å: Chain A: R.295, Q.321, E.323, H.347, R.367, K.371, F.375, Y.379 Chain B: G.12 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.321, A:Q.321, A:Y.379, A:Y.379, A:Y.379 Water bridges: A:R.295 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Cation interactions: A:R.295, A:F.375

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: T.252, Y.253, L.257, P.287, N.288 Chain C: C.9, C.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.288 Water bridges: A:D.286 GOL.3: 3 residues within 4Å: Chain A: R.21, W.26, L.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.21, A:R.21 GOL.4: 3 residues within 4Å: Chain A: R.133, W.136, F.432 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.133 GOL.5: 4 residues within 4Å: Chain B: C.6, G.7, G.8 Chain C: C.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Obeid, S. et al., Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase. J.Biol.Chem. (2012)

Release Date

2012-02-15

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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