SMTL ID : 4qwc.1 (1 other biounit)

Ternary Crystal Structures of a Y-family DNA polymerase DPO4 from Sulfobus Solfataricus in Comples with DNA and L-DCDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

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

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: R.279, I.341, E.342 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.342 Hydrogen bonds: A:E.342 ACT.4: 5 residues within 4Å: Chain A: A.181, V.183, I.186, G.187 Chain B: T.12 No protein-ligand interaction detected (PLIP)

1 x LTP: 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one(Non-covalent)

LTP.5: 18 residues within 4Å: Chain A: D.7, F.8, D.9, Y.10, F.11, Y.12, A.44, T.45, R.51, A.57, I.104, D.105, K.159 Chain B: C.13 Chain C: G.5, G.6 Ligands: CA.1, CA.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.57 Hydrogen bonds: A:F.11, A:T.45 Water bridges: A:Y.10, A:Y.48, A:R.51, A:S.103, A:S.103 Salt bridges: A:R.51, A:R.51, A:K.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gaur, V. et al., Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res. (2014)

Release Date

2014-08-27

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

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