SMTL ID : 5tbb.1

Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)FTC and PPi.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 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.4 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.36

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.192, D.194 Ligands: NA.5, PPV.8, 43X.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.192, A:D.194

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

NA.3: 7 residues within 4Å: Chain A: T.103, V.105, S.106, G.107, I.108 Chain B: G.9 Ligands: ACT.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.105, A:G.107, A:I.108 NA.4: 5 residues within 4Å: Chain A: K.62, K.63, L.64, V.67 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.67, A:V.67 NA.5: 6 residues within 4Å: Chain A: D.192, D.194, D.258 Chain B: C.10 Ligands: MN.2, 43X.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.258 NA.7: 6 residues within 4Å: Chain A: N.30, V.31, Q.33, I.99, P.110, R.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.33

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 7 residues within 4Å: Chain A: T.103, R.104, V.105, S.106 Chain B: G.9, C.10 Ligands: NA.3 No protein-ligand interaction detected (PLIP) ACT.9: 3 residues within 4Å: Chain A: F.322, D.323, Y.324 No protein-ligand interaction detected (PLIP)

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.8: 9 residues within 4Å: Chain A: R.151, G.181, S.182, R.185, G.191, D.192, D.194 Ligands: MN.2, 43X.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.151, A:S.182, A:G.191 Salt bridges: A:R.185

1 x 43X: [(2R,5S)-5-(4-amino-5-fluoro-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate(Non-covalent)

43X.10: 11 residues within 4Å: Chain A: D.192, D.194, R.260, Y.273, F.274 Chain B: C.10 Chain C: G.6, G.7 Ligands: MN.2, NA.5, PPV.8 No protein-ligand interaction detected (PLIP)

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

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