SMTL ID : 1n48.1

Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

CA.1: 3 residues within 4Å: Chain A: T.12, A.13 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) CA.3: 6 residues within 4Å: Chain A: A.13 Chain C: D.7, D.105, E.106 Ligands: ATP.2, CA.4 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.7, C:D.105, C:D.105, C:E.106, H2O.1 CA.4: 5 residues within 4Å: Chain C: D.7, F.8, D.105 Ligands: ATP.2, CA.3 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.7, C:D.7, C:F.8, C:D.105, H2O.6

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 20 residues within 4Å: Chain A: T.12, A.13 Chain B: T.4, A.5 Chain C: D.7, F.8, D.9, Y.10, Y.12, A.44, T.45, Y.48, R.51, A.57, G.58, D.105, K.159 Ligands: CA.1, CA.3, CA.4 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Y.12, C:T.45 Hydrogen bonds: C:Y.10 Water bridges: C:D.9, C:D.9, C:D.9, C:F.11, C:F.11, C:K.152, C:K.152, C:D.156, C:D.156 Salt bridges: C:R.51, C:K.159, C:K.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ling, H. et al., A Y-family polymerase complexed with abasic lesions: catching DNA with a loaded nucleoside triphosphate. To be Published

Release Date

2004-02-24

Peptides

DNA polymerase IV: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase IV

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