SMTL ID : 4qwa.1

TERNARY CRYSTAL STRUCTURES OF A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS in COMPLEX WITH DNA AND (-)3TC-DP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x 0G8: [(2R,5S)-5-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-1,3-OXATHIOLAN-2-YL]METHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

0G8.1: 16 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 Chain B: C.13 Chain C: G.3, G.4 Ligands: CA.2, CA.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.57 Hydrogen bonds: A:D.7, A:F.11, A:T.45 Water bridges: A:Y.10, A:Y.10, A:Y.12, A:Y.12, A:A.46 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: 0G8.1, 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.6 CA.3: 5 residues within 4Å: Chain A: D.7, F.8, D.105 Ligands: 0G8.1, CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.7, A:F.8, A:D.105, A:D.105, H2O.3 CA.4: 2 residues within 4Å: Chain A: A.181, I.186 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.181, A:I.186, H2O.4, H2O.6, H2O.9

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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