SMTL ID : 3rwu.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 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, L.415, Y.416, P.417, 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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:L.415, A:Y.416, A:N.564 Water bridges: A:D.411 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: ATP.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: 6 residues within 4Å: Chain A: D.411, D.623, S.624 Chain C: C.13 Ligands: ATP.1, CA.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.411, A:D.623 CA.4: 3 residues within 4Å: Chain A: N.505, N.507, K.531 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.505, A:K.531 CA.5: 2 residues within 4Å: Chain A: D.114, E.116 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.116, H2O.5, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Hydrogen-Bonding Capability of a Templating Difluorotoluene Nucleotide Residue in an RB69 DNA Polymerase Ternary Complex. J.Am.Chem.Soc. (2011)

Release Date

2011-06-29

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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