SMTL ID : 5u2s.1

Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)3TC-TP and Ca2+.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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: 20 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, ACT.8, ACT.11 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:H.136, A:T.235, A:T.235, A:K.236, A:K.236, A:K.236, A:K.236, A:Y.273, A:Y.273, A:Y.273, A:Y.298 Water bridges: A:N.39, A:N.135, A:H.137, A:Y.273, A:K.282, A:E.297 pi-Stacking: A:H.36

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

1RZ.2: 18 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, G.276, D.278, N.281, R.285 Chain B: C.10 Chain C: G.6 Ligands: CA.3, NA.13 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:G.191, A:D.192, A:D.278, A:R.285 Water bridges: A:D.278, A:K.282, A:K.282, A:K.282 Salt bridges: A:R.151, A:R.185

1 x CA: CALCIUM ION(Non-covalent)

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

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

NA.4: 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.5: 6 residues within 4Å: Chain A: T.103, V.105, S.106, I.108 Chain B: G.9 Ligands: ACT.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.105, A:I.108 NA.6: 3 residues within 4Å: Chain A: N.26, K.29, N.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.29, A:K.29, A:N.30 NA.13: 2 residues within 4Å: Chain B: C.10 Ligands: 1RZ.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.192, A:D.194

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

ACT.7: 7 residues within 4Å: Chain A: T.103, R.104, V.105, S.106 Chain B: G.9, C.10 Ligands: NA.5 No protein-ligand interaction detected (PLIP) ACT.8: 6 residues within 4Å: Chain A: H.36, N.39, A.40, K.43 Chain C: C.5 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.39 ACT.9: 5 residues within 4Å: Chain A: D.132, K.133, L.134, N.135, R.139 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.135 Salt bridges: A:R.139 ACT.10: 4 residues within 4Å: Chain A: A.112, N.135, Q.138 Chain B: C.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.138 Salt bridges: A:K.115 ACT.11: 4 residues within 4Å: Chain A: K.43, P.65 Ligands: DG-DT-DC-DG-DG.1, DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.65 Salt bridges: A:K.43 ACT.12: 3 residues within 4Å: Chain A: R.91, Q.92, S.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.97

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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