SMTL ID : 4e3s.1

RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

1 x QTP: 3-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7-methyl-3H-imidazo[4,5-b]pyridine(Non-covalent)

QTP.1: 18 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: T.3, G.4 Chain C: C.13 Ligands: CA.2, CA.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:L.415, A:Y.416, A:N.564, A:D.623 Water bridges: A:D.411, A:K.486, A:K.486, A:K.560 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: QTP.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: 5 residues within 4Å: Chain A: D.411, D.623 Chain C: C.13 Ligands: QTP.1, CA.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.411, A:D.623, H2O.11 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.2, H2O.9, H2O.11 CA.5: 2 residues within 4Å: Chain A: E.686, E.716 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.716, H2O.5, H2O.9, H2O.15 CA.6: 1 residues within 4Å: Chain A: E.116 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.116, A:E.116, H2O.3, H2O.15, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA. Biochemistry (2012)

Release Date

2012-05-23

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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