SMTL ID : 4qw9.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x 0G4: [[[[(2R,5S)-5-(4-AZANYL-5-FLUORANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-1,3-OXATHIOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]AMINO]PHOSPHONIC ACID(Non-covalent)

0G4.1: 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 C: G.3, G.4 Chain B: C.13 Ligands: CA.2, CA.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.10, A:F.11, A:R.51, A:R.51, A:K.159, A:K.159 Water bridges: A:D.9, A:D.9, A:D.9, A:T.45

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: 0G4.1, CA.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.7, A:D.105, A:E.106, H2O.1506 CA.3: 5 residues within 4Å: Chain A: D.7, F.8, D.105 Ligands: 0G4.1, CA.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.7, A:F.8, A:D.105, A:D.105 CA.4: 2 residues within 4Å: Chain A: A.181, I.186 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.181, H2O.1508, H2O.1508

Links

RCSB   PDBe   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)

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

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