SMTL ID : 3suq.1

RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite 2AP (AT rich sequence)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

monomer

Ligands

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

DCP.1: 19 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, L.415, Y.416, P.417, R.482, K.486, K.560, N.564, T.622, D.623 Chain B: G.2, T.3 Chain C: A.13 Ligands: CA.2, CA.3, CA.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:L.412, A:S.414, A:L.415, A:Y.416, A:N.564, A:N.564, A:D.623 Salt bridges: A:R.482, A:K.486, 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: DCP.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: 4 residues within 4Å: Chain A: D.411, D.623 Ligands: DCP.1, CA.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.411, A:D.623 CA.4: 4 residues within 4Å: Chain A: N.505, P.506, N.507, K.531 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.505, A:K.531 CA.5: 5 residues within 4Å: Chain A: D.411, K.486, E.686, E.716 Ligands: DCP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.411 CA.6: 2 residues within 4Å: Chain A: D.114, E.116 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reha-Krantz, L.J. et al., Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase. Biochemistry (2011)

Release Date

2011-11-09

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase