SMTL ID : 4dtm.1

RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddG/dC as the Penultimate Base-pair

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

DCP.1: 16 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, L.415, Y.416, R.482, K.486, K.560, N.564, T.622, D.623 Chain B: C.5 Chain C: G.13 Ligands: CA.2, CA.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:L.415, A:Y.416, A:N.564, A:N.564 Water bridges: A:R.482, A:K.560, A:K.560, A:K.560, A:K.560, A:G.568 Salt bridges: A:R.482, A:K.486, A:K.560, A:K.560

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: DCP.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.411, A:D.411, A:L.412, A:D.623, H2O.4 CA.3: 4 residues within 4Å: Chain A: D.411, D.623 Chain C: G.13 Ligands: DCP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.623, H2O.4 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: 2 residues within 4Å: Chain A: D.411, E.716 No protein-ligand interaction detected (PLIP) 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.2, H2O.11

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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