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

Bypass of a bulky adduct dG1,8 by DPO4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

DCP.1: 17 residues within 4Å: Chain A: D.7, F.8, D.9, Y.10, F.11, Y.12, A.44, T.45, Y.48, R.51, A.57, D.105, K.159 Chain B: G.3, X.5 Ligands: CA.2, CA.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.12, A:A.57 Hydrogen bonds: A:F.8, A:Y.10, A:F.11, A:Y.12, A:T.45, A:T.45, A:Y.48, A:Y.48 Water bridges: A:D.9, A:A.57, A:E.106, A:K.159, A:K.159 Salt bridges: A:R.51, A:R.51, A:K.159, A:K.159, A:K.159

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.7, F.8, D.105, K.159 Ligands: DCP.1, CA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.7, A:F.8, A:D.105 CA.3: 5 residues within 4Å: Chain A: D.7, D.105, E.106 Ligands: DCP.1, CA.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.7, A:D.105, A:E.106, H2O.1, H2O.1

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: A.181, I.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.186

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: L.19, V.80, Q.83, V.84, R.87 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.83, A:R.87, A:R.87 Water bridges: A:E.136, A:E.136 GOL.6: 5 residues within 4Å: Chain A: E.100, K.148, V.149, Y.233, R.240 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.100, A:K.148, A:Y.233, A:R.240 Water bridges: A:Y.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vyas, R. et al., Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase. J.Am.Chem.Soc. (2015)

Release Date

2015-09-16

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

DNA polymerase IV

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