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

Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain C: D.7, F.8, D.105 Ligands: TMP.3 6 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:D.7, C:F.8, C:D.105, H2O.1, H2O.5, TMP.3 CA.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.4, H2O.4

1 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.3: 15 residues within 4Å: Chain A: T.14 Chain B: T.2, A.3 Chain C: F.8, D.9, Y.10, F.11, Y.12, A.44, T.45, R.51, A.57, D.105 Ligands: CA.1, GOL.4 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:A.57 Hydrogen bonds: C:Y.10, C:F.11, C:T.45 Water bridges: C:Y.12, C:Y.12, C:R.51, C:R.51, C:K.159, C:K.159, C:K.159, C:K.159 Salt bridges: C:R.51

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain C: K.56, A.57 Ligands: TMP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wong, J.H. et al., Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4. J.Mol.Biol. (2008)

Release Date

2008-06-24

Peptides

DNA polymerase IV: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase IV

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