SMTL ID : 3qer.1

RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dATP Opposite Difluorotoluene Nucleoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 16 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, L.415, Y.416, R.482, K.560, N.564, T.622, D.623 Chain B: N.4, G.5 Chain C: C.13 Ligands: CA.2, CA.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:D.411, A:S.414, A:L.415, A:Y.416, A:N.564 Water bridges: A:R.482, A:K.486, A:K.486, A:K.486, A:K.560 Salt bridges: A:R.482, A:K.486, A:K.560, A:K.560, A:K.560

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: DTP.1, CA.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.411, A:D.411, A:L.412, A:D.623 CA.3: 5 residues within 4Å: Chain A: D.411, D.623 Chain C: C.13 Ligands: DTP.1, CA.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.411, A:D.623, H2O.5 CA.4: 3 residues within 4Å: Chain A: N.505, N.507, K.531 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.505, A:K.531, H2O.2, H2O.3, H2O.32 CA.5: 1 residues within 4Å: Chain A: E.116 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.116, H2O.3, H2O.25, H2O.27, H2O.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Structural Basis for Differential Insertion Kinetics of dNMPs Opposite a Difluorotoluene Nucleotide Residue. Biochemistry (2012)

Release Date

2012-01-25

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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