SMTL ID : 7f4y.1

Crystal structure of replisomal dimer of DNA polymerase from bacteriophage RB69 with DNA duplexes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

1 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.1: 17 residues within 4Å: Chain A: D.416, L.417, T.418, S.419, L.420, Y.421, P.422, R.487, K.565, N.569, Y.572, T.627, D.628 Chain B: A.4, G.5 Chain C: C.15 Ligands: CA.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.421 Hydrogen bonds: A:L.417, A:S.419, A:L.420, A:Y.421, A:K.565, A:N.569, A:N.569, A:D.628 Water bridges: A:R.487, A:R.487 Salt bridges: A:R.487, A:K.491, A:K.565

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.416, L.417, D.628 Ligands: DUP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.416, A:L.417, A:D.628 CA.4: 1 residues within 4Å: Chain D: M.905 No protein-ligand interaction detected (PLIP)

2 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.3: 15 residues within 4Å: Chain A: Y.38, S.41, F.43, K.53, Y.54, R.64, G.89, M.90, A.96, D.100, F.375, K.379, K.383, V.384, I.385 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.38, A:M.90, A:D.100, A:K.383, A:K.383, A:I.385 Water bridges: A:S.41, A:R.64 Salt bridges: A:K.53, A:R.64 pi-Stacking: A:F.375 5GP.5: 15 residues within 4Å: Chain D: Y.38, S.41, F.43, K.53, Y.54, R.64, G.89, M.90, A.96, D.100, F.375, K.379, K.383, V.384, I.385 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Y.54, D:M.90, D:D.100, D:K.383, D:K.383, D:I.385 Salt bridges: D:K.53, D:R.64 pi-Stacking: D:F.375

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain D: F.769, E.773 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.773, H2O.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69. Front Mol Biosci (2021)

Release Date

2021-07-14

Peptides

DNA polymerase: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

DNA polymerase