SMTL ID : 5tbc.1

PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTRATE, INCORPORATED (-)3TC-MP AND AN ANOTHER INCOMING (-)3TC-TP NUCLEOTIDE.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER(Non-covalent)

DG-DT-DC-DG-DG.1: 18 residues within 4Å: Chain A: H.36, K.37, A.40, Y.41, L.64, P.65, G.66, V.67, G.68, T.69, K.70, I.71 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: NA.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.39 pi-Stacking: A:H.36

1 x 1RZ: Lamivudine Triphosphate(Non-covalent)

1RZ.2: 17 residues within 4Å: Chain A: R.151, G.181, S.182, R.185, S.189, S.190, G.191, D.192, Y.273, F.274, T.275, G.276, S.277, D.278, N.281 Ligands: NA.3, 42E.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:S.189, A:G.191, A:D.192, A:N.281 Water bridges: A:D.278 Salt bridges: A:R.151, A:R.185

6 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: D.192 Ligands: 1RZ.2, 42E.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192 NA.4: 6 residues within 4Å: Chain A: T.103, V.105, G.107, I.108 Chain B: G.9 Ligands: NA.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.105, A:G.107, A:I.108 NA.5: 6 residues within 4Å: Chain A: K.62, L.64, P.65, G.66, V.67 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.64, A:G.66, A:V.67 NA.6: 1 residues within 4Å: Chain A: S.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.32 NA.7: 3 residues within 4Å: Chain A: T.103, R.104 Ligands: NA.4 No protein-ligand interaction detected (PLIP) NA.10: 2 residues within 4Å: Chain C: G.9, C.10 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 4 residues within 4Å: Chain A: A.34, I.35, H.36, K.37 Ligand excluded by PLIP

1 x 42E: [(2R,5S)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate(Non-covalent)

42E.9: 8 residues within 4Å: Chain A: D.192, R.260, Y.273 Chain B: C.10 Chain C: G.6, G.7 Ligands: 1RZ.2, NA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reed, A.J. et al., Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc. (2017)

Release Date

2017-01-11

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

Related Entries With Identical Sequence