SMTL ID : 4qw8.1

TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND D-DCTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

monomer

Ligands

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

DCP.1: 16 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, D.105, K.159 Chain B: C.13 Chain C: G.3 Ligands: CA.2, CA.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.12 Hydrogen bonds: A:F.8, A:Y.10, A:F.11, A:Y.12, A:T.45 Water bridges: A:D.9, A:D.9 Salt bridges: A:R.51, A:R.51, A:K.159

3 x CA: CALCIUM ION(Non-covalent)

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

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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