SMTL ID : 3rax.1 (1 other biounit)

Dpo4 extension ternary complex with 3'-terminal primer T base opposite the 1-methylguanine (M1G) lesion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 20 residues within 4Å: Chain A: D.7, F.8, D.9, Y.10, F.11, Y.12, V.32, A.44, T.45, Y.48, R.51, A.57, I.104, D.105, K.159 Chain B: T.13 Chain C: C.6, G.7 Ligands: CA.2, CA.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.12 Hydrogen bonds: A:D.7, A:Y.10, A:F.11, A:Y.12 Water bridges: A:D.9, A:R.51, A:K.159, A:K.159, A:K.159 Salt bridges: A:R.51, A:R.51, A:K.159, A:K.159

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.7, D.105, E.106 Chain B: T.13 Ligands: DGT.1, CA.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.7, A:D.105, A:E.106, H2O.3, H2O.5 CA.3: 5 residues within 4Å: Chain A: D.7, F.8, D.105 Ligands: DGT.1, CA.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.7, A:D.7, A:F.8, A:D.105 CA.4: 2 residues within 4Å: Chain A: A.181, I.186 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.181, A:I.186, H2O.3, H2O.11, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rechkoblit, O. et al., Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions. Structure (2011)

Release Date

2011-06-15

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

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