SMTL ID : 2va2.1 (1 other biounit)

Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 4 residues within 4Å: Chain A: D.13, F.14, D.111 Ligands: DCT.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.13, A:F.14, A:D.111, H2O.4 CA.2: 2 residues within 4Å: Chain A: A.187, I.192 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.187, A:I.192, H2O.1, H2O.2, H2O.4 CA.4: 1 residues within 4Å: Ligands: DCT.3 No protein-ligand interaction detected (PLIP)

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.3: 17 residues within 4Å: Chain A: D.13, F.14, D.15, Y.16, A.50, T.51, Y.54, R.57, A.63, G.64, D.111, K.165 Chain B: A.13 Chain C: G.5, N.6 Ligands: CA.1, CA.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.63 Hydrogen bonds: A:Y.16, A:A.63 Water bridges: A:F.14, A:F.17, A:T.51, A:K.165 Salt bridges: A:R.57, A:R.57, A:K.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Irimia, A. et al., Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4- Difluorotoluene. J.Biol.Chem. (2007)

Release Date

2007-10-30

Peptides

DNA POLYMERASE IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA POLYMERASE IV

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