SMTL ID : 4m45.1

RB69 DNA polymerase ternary complex with dG/dT at position n-5 of primer/template duplex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 17 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, A.415, Y.416, P.417, R.482, K.560, N.564, T.622, D.623 Chain B: T.2, G.3 Chain C: C.13 Ligands: CA.2, CA.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:A.415, A:Y.416, A:N.564 Water bridges: A:R.482, A:R.482, A:K.486, A:Q.556, A:K.560, A:E.716, A:E.716 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: ATP.1, CA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.411, A:L.412, A:D.623 CA.3: 6 residues within 4Å: Chain A: D.411, D.623, S.624 Chain C: C.13 Ligands: ATP.1, CA.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.623, H2O.6 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.5, H2O.8, H2O.8 CA.5: 1 residues within 4Å: Chain A: E.716 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: E.116, I.309 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.116, A:E.116, H2O.19, H2O.19, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant. Protein Sci. (2014)

Release Date

2014-02-12

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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