SMTL ID : 6uok.2 (1 other biounit)

Y271G DNA polymerase beta substrate complex with templating cytosine and incoming r8-oxo-GTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: DNA (5'-D(P*GP*TP*CP*GP*G)-3')(Non-covalent)

DG-DT-DC-DG-DG.1: 19 residues within 4Å: Chain A: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69 Chain B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.3, MG.8 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.34

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: P.50, H.51 No protein-ligand interaction detected (PLIP)

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

NA.3: 4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.60, A:G.64, A:V.65 Water bridges: A:K.60 NA.4: 4 residues within 4Å: Chain A: T.101, V.103, I.106 Chain C: G.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.106 NA.7: 5 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: C.10 Ligands: 8GT.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.192, A:D.256

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

MN.5: 3 residues within 4Å: Chain A: D.190, D.192 Ligands: 8GT.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.1

1 x 8GT: 8-OXO-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

8GT.6: 16 residues within 4Å: Chain A: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192, G.271, F.272, D.276 Chain B: C.6, G.7 Chain C: C.10 Ligands: MN.5, NA.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.180, A:S.180, A:S.180, A:R.183, A:G.189, A:D.190, A:D.276 Salt bridges: A:R.149

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.8: 1 residues within 4Å: Ligands: DG-DT-DC-DG-DG.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, M.R. et al., Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta. J.Biol.Chem. (2020)

Release Date

2020-01-08

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

Related Entries With Identical Sequence