SMTL ID : 4qwe.1

TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)FTC-DP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x FTD: [(2R,5S)-5-(4-amino-5-fluoro-2-oxo-3,6-dihydropyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl trihydrogen diphosphate(Non-covalent)

FTD.1: 17 residues within 4Å: Chain A: D.7, F.8, 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.3, G.4 Ligands: CA.2, CA.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:F.11, A:T.45 Water bridges: A:Y.10, A:Y.10, A:R.51, A:A.57, A:K.159 Salt bridges: A:R.51, A:R.51, A:K.159

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.7, D.105, E.106 Chain B: C.13 Ligands: FTD.1, CA.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.106, H2O.7 CA.3: 5 residues within 4Å: Chain A: D.7, F.8, D.105 Ligands: FTD.1, CA.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.7, A:F.8, A:D.105, H2O.3 CA.4: 2 residues within 4Å: Chain A: A.181, I.186 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.181, A:I.186, H2O.4, H2O.6

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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