SMTL ID : 1sl2.1

Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain C: D.469, A.470, G.472, L.473, D.648 Ligands: DAD.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:A.470, C:D.648 MG.2: 5 residues within 4Å: Chain A: A.22 Chain C: D.469, D.648, H.698 Ligands: DAD.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.469, C:D.648, H2O.2 MG.3: 1 residues within 4Å: Chain C: D.5 No protein-ligand interaction detected (PLIP)

1 x DAD: 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

DAD.4: 16 residues within 4Å: Chain A: A.22 Chain B: T.4 Chain C: R.423, D.469, A.470, S.471, G.472, L.473, E.474, H.500, R.512, K.516, Y.520, D.648 Ligands: MG.1, MG.2 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:E.474, C:Y.520 Hydrogen bonds: C:R.423, C:G.472, C:L.473, C:Y.520 Water bridges: C:K.516, C:K.516, C:K.516, C:K.516, C:N.605 Salt bridges: C:H.500, C:H.500, C:R.512, C:K.516, C:K.516, C:K.516 pi-Stacking: C:Y.520

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7. Nat.Struct.Mol.Biol. (2004)

Release Date

2004-07-06

Peptides

DNA polymerase: C
Thioredoxin 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

DNA polymerase

Thioredoxin 1

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