SMTL ID : 4tqs.2 (1 other biounit)

Ternary complex of Y-family DNA polymerase Dpo4 with (5'S)-8,5'-Cyclo-2'-deoxyguanosine and dCTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.1: 20 residues within 4Å: Chain A: D.13, F.14, D.15, Y.16, F.17, Y.18, A.50, T.51, Y.54, R.57, A.63, G.64, D.111, K.165 Chain B: T.12 Chain C: G.6, A.7 Ligands: MG.2, MG.3, DOC.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.63 Hydrogen bonds: A:Y.16, A:F.17, A:T.51 Water bridges: A:A.63, A:E.112, A:K.165, A:K.165 Salt bridges: A:R.57, A:R.57, A:K.165

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.13, D.111, E.112 Ligands: DCP.1, MG.3, DOC.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.13, A:D.111, A:D.111, A:E.112, H2O.9 MG.3: 5 residues within 4Å: Chain A: D.13, F.14, D.111 Ligands: DCP.1, MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.13, A:D.13, A:F.14, A:D.111

1 x DOC: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DOC.4: 11 residues within 4Å: Chain A: A.108, D.111, E.112, K.158, G.191 Chain B: T.11, T.12 Chain C: C.10, C.11 Ligands: DCP.1, MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.112 Water bridges: A:S.109, A:K.158, A:K.158, A:K.158, A:K.227, A:K.227, A:K.227, A:K.227 Salt bridges: A:K.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, W. et al., Kinetic and Structural Mechanisms of (5'S)-8,5'-Cyclo-2'-deoxyguanosine-Induced DNA Replication Stalling. Biochemistry (2015)

Release Date

2015-01-14

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA polymerase IV

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