SMTL ID : 5u2t.1

Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)FTC-TP and Ca2+.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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: 19 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, K.74 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: NA.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.39 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: 16 residues within 4Å: Chain A: R.151, G.181, S.182, R.185, S.190, G.191, D.192, D.194, Y.273, F.274, D.278, N.281 Chain B: C.10 Chain C: G.6 Ligands: CA.3, NA.10 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:S.182, A:G.191, A:D.192, A:N.281 Water bridges: A:D.192, A:D.192 Salt bridges: A:R.151, A:R.185

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.192, D.194 Ligands: 1RY.2, NA.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:D.194, H2O.1, H2O.2

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

NA.4: 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:V.105, A:G.107, A:I.108 NA.5: 1 residues within 4Å: Chain A: S.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.32 NA.6: 4 residues within 4Å: Chain A: K.62, 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.10: 4 residues within 4Å: Chain A: D.194 Chain B: C.10 Ligands: 1RY.2, CA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192 NA.11: 2 residues within 4Å: Chain B: T.3, G.4 No protein-ligand interaction detected (PLIP)

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

ACT.7: 4 residues within 4Å: Chain A: K.62, T.69, A.72, E.73 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.62, A:A.72 Salt bridges: A:K.62 ACT.8: 2 residues within 4Å: Chain A: K.43, S.46 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.46, A:S.46 Salt bridges: A:K.50 ACT.9: 2 residues within 4Å: Chain A: R.154, L.158 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vyas, R. et al., Structural basis for the D-stereoselectivity of human DNA polymerase beta. Nucleic Acids Res. (2017)

Release Date

2017-05-24

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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