SMTL ID : 2w9c.1 (1 other biounit)

Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.111, E.112 Ligands: MG.2, TTP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.111, A:D.111, H2O.1 MG.2: 5 residues within 4Å: Chain A: D.13, F.14, D.111 Ligands: MG.1, TTP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.13, A:F.14, A:D.111 MG.3: 4 residues within 4Å: Chain A: A.187, I.192, G.193 Chain B: C.13 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.187, A:I.192, H2O.2, H2O.2

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.4: 18 residues within 4Å: Chain A: D.13, F.14, D.15, Y.16, F.17, A.50, T.51, Y.54, R.57, A.63, D.111, E.112, K.165 Chain B: C.13 Chain C: G.5, G.6 Ligands: MG.1, MG.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.63 Hydrogen bonds: A:Y.16, A:F.17, A:Y.54, A:Y.54, A:R.57 Water bridges: A:F.14, A:D.111, A:D.111, A:K.165 Salt bridges: A:R.57, A:R.57, A:K.165, A:K.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes. J.Biol.Chem. (2009)

Release Date

2009-05-12

Peptides

DNA POLYMERASE IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA POLYMERASE IV

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