SMTL ID : 4jv2.1

Ternary complex of gamma-OHPDG adduct modified dna with dna (-1 primer) polymerase iv and incoming datp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

monomer

Ligands

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 17 residues within 4Å: Chain A: D.13, F.14, D.15, Y.16, F.17, Y.18, A.50, T.51, Y.54, R.57, A.63, D.111, E.112, K.165 Chain B: T.1, X.2 Ligands: CA.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.18, A:T.51 Hydrogen bonds: A:D.13, A:F.14, A:D.15, A:Y.16, A:F.17, A:Y.18 Salt bridges: A:R.57, A:R.57, A:K.165

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.13, F.14, D.15, D.111 Ligands: DTP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.13, A:F.14, A:D.111 CA.3: 2 residues within 4Å: Chain A: A.187, I.192 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.187, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shanmugam, G. et al., Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4. Chem.Res.Toxicol. (2013)

Release Date

2013-08-28

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

Related Entries With Identical Sequence