SMTL ID : 3qep.1

RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dTTP Opposite Difluorotoluene Nucleoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.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 17 PLIP interactions: 17 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, A:R.482, A:R.482, A:R.482, A:K.486, A:K.486, A:K.486 Salt bridges: A:R.482, A:K.486, A:K.560, A:K.560, A:K.560

7 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: TTP.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: TTP.1, CA.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.411, A:D.623, H2O.3, H2O.13 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.12, H2O.17, H2O.31 CA.5: 1 residues within 4Å: Chain A: E.116 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.116, H2O.11, H2O.12, H2O.14, H2O.31 CA.6: 1 residues within 4Å: Chain A: D.792 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.792, H2O.31, H2O.38, H2O.38 CA.7: 2 residues within 4Å: Chain A: E.660, D.684 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.684, H2O.11, H2O.34 CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

2011-08-31

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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