SMTL ID : 4dtn.1

RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

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

DTP.1: 15 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: T.4 Chain C: A.13 Ligands: CA.2, CA.3 15 PLIP interactions: 15 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.560 Salt bridges: A:R.482, A:K.486, A:K.560, A:K.560, A:K.560

5 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: A.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.10 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.1, H2O.9, H2O.16 CA.5: 1 residues within 4Å: Chain A: E.716 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.716, H2O.15, H2O.22, H2O.23 CA.6: 1 residues within 4Å: Chain A: E.116 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.116, A:E.116, H2O.5, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA. Biochemistry (2012)

Release Date

2012-06-06

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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