SMTL ID : 1jx4.1

Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain C: D.7, F.8, D.105 Ligands: ADI.3 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.7, C:F.8, C:D.105, H2O.15

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain C: A.181, I.186 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.181, C:I.186, H2O.1, H2O.396, H2O.398

1 x ADI: 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADI.3: 18 residues within 4Å: Chain A: A.13 Chain B: T.5, T.6 Chain C: D.7, F.8, Y.10, F.11, Y.12, A.44, T.45, Y.48, R.51, A.57, G.58, M.76, D.105, K.159 Ligands: CA.1 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.12 Hydrogen bonds: C:F.11, C:Y.48 Water bridges: C:Y.10, C:T.45, C:T.45, C:R.51, C:R.51, C:A.57, C:K.159 Salt bridges: C:R.51, C:R.51, C:K.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ling, H. et al., Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell(Cambridge,Mass.) (2001)

Release Date

2001-10-05

Peptides

DNA polymerase IV (family Y): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase IV (family Y)

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