SMTL ID : 3pr4.1

Dpo4 Y12A mutant incorporating dADP opposite template dT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: D.7, F.8, D.9, Y.10, F.11, A.12, A.44, T.45, Y.48, R.51, A.57, D.105, K.159 Chain B: C.13 Chain C: T.5, G.6 Ligands: CA.2, CA.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.45 Hydrogen bonds: A:Y.10, A:F.11, A:A.12, A:T.45, A:Y.48, A:Y.48 Water bridges: A:R.51, A:R.51 Salt bridges: A:R.51, A:R.51, A:K.159

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.7, F.8, D.105 Ligands: ATP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.7, A:F.8, A:D.105, H2O.2 CA.3: 5 residues within 4Å: Chain A: D.7, E.106, K.159 Chain B: C.13 Ligands: ATP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.7, A:E.106, H2O.2 CA.4: 3 residues within 4Å: Chain A: A.181, I.186 Chain B: T.12 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.181, A:I.186, H2O.2, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirouac, K.N. et al., Structural mechanism of ribonucleotide discrimination by a Y-family DNA polymerase. J.Mol.Biol. (2011)

Release Date

2011-02-23

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

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