SMTL ID : 3sz2.1

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dG as templating nucleobase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 6 residues within 4Å: Chain A: E.170, V.171, E.174, L.246, L.298, R.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.170, A:R.301 FMT.2: 4 residues within 4Å: Chain A: S.447, E.450, A.451, R.454 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.450, A:E.450, A:R.454, A:R.454 FMT.3: 7 residues within 4Å: Chain A: T.252, Y.253, P.287, N.288, N.291 Chain C: C.9 Ligands: FMT.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.288, A:N.291 Water bridges: A:D.286, A:N.288 FMT.6: 7 residues within 4Å: Chain A: N.193, S.194, R.195, D.196 Chain B: G.7 Chain C: G.11, T.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.195 Water bridges: A:S.194, A:D.196 FMT.7: 3 residues within 4Å: Chain C: C.5, G.6, C.7 No protein-ligand interaction detected (PLIP) FMT.8: 9 residues within 4Å: Chain A: T.252, Y.253, P.256, L.257, L.260, P.287 Chain C: C.9, C.10 Ligands: FMT.3 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 1 residues within 4Å: Chain B: G.8 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: K.22, D.286 Chain C: C.9, C.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Betz, K. et al., KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry. Nat.Chem.Biol. (2012)

Release Date

2012-06-06

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

Related Entries With Identical Sequence