SMTL ID : 5tb9.1

Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)FTC-TP and Mn2+.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 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: 16 residues within 4Å: Chain A: H.36, K.37, A.40, Y.41, P.65, G.66, V.67, G.68, T.69, K.70, I.71 Chain C: C.2, G.3, A.4, C.5 Ligands: NA.11 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.282, A:R.285, A:R.285, A:R.285 Water bridges: A:H.36 Salt bridges: A:K.282 pi-Stacking: A:H.36

1 x 1RY: [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

1RY.2: 18 residues within 4Å: Chain A: G.181, S.182, R.185, S.190, G.191, D.192, D.194, D.258, Y.273, F.274, G.276, D.278, N.281 Chain B: C.10 Chain C: G.6 Ligands: MN.3, MN.4, ACT.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:G.191, A:D.192, A:N.281 Salt bridges: A:R.185

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

MN.3: 6 residues within 4Å: Chain A: D.192, D.194, D.258 Chain B: C.10 Ligands: 1RY.2, MN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.194, A:D.258, H2O.1 MN.4: 4 residues within 4Å: Chain A: D.192, D.194 Ligands: 1RY.2, MN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.194, H2O.1 MN.5: 2 residues within 4Å: Chain A: H.339, H.341 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.339, A:H.341, H2O.2, H2O.2, H2O.2 MN.6: 2 residues within 4Å: Chain A: T.12, H.342 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.342, H2O.3 MN.7: 1 residues within 4Å: Chain A: E.119 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.119 MN.8: 3 residues within 4Å: Chain A: K.50, H.338, H.340 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.50, A:H.338, A:H.340, H2O.2

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

NA.9: 1 residues within 4Å: Chain A: D.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.132 NA.10: 3 residues within 4Å: Chain A: Y.144, D.147, H.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.254 NA.11: 4 residues within 4Å: Chain A: K.62, L.64, V.67 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.64 NA.14: 4 residues within 4Å: Chain A: T.103, V.105, I.108 Chain B: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.107, A:I.108, A:I.108

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

ACT.12: 1 residues within 4Å: Ligands: 1RY.2 No protein-ligand interaction detected (PLIP) ACT.13: 4 residues within 4Å: Chain A: A.34, I.35, H.36, K.37 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.36, A:K.37 Water bridges: A:I.35 Salt bridges: A:H.36 ACT.15: 1 residues within 4Å: Chain C: C.2 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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