SMTL ID : 6uol.1

Y271G DNA polymerase beta substrate complex with a templating cytosine and incoming rGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 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: 18 residues within 4Å: Chain A: C.1, C.2, G.3, A.4, C.5 Chain C: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69 Ligands: NA.8 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:K.280 Hydrogen bonds: C:R.283 Water bridges: C:N.37, C:R.40, C:R.40 Salt bridges: C:K.280 pi-Stacking: C:H.34

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

EDO.2: 7 residues within 4Å: Chain C: K.148, R.149, P.151, E.154, Y.250, P.251, R.253 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.253, C:R.253 Water bridges: C:E.154, C:E.154

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

MN.3: 2 residues within 4Å: Chain C: H.285, E.288 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.285, C:E.288, H2O.8 MN.4: 1 residues within 4Å: Chain C: H.222 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.222 MN.5: 2 residues within 4Å: Chain C: D.145, H.252 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.145, C:H.252, H2O.6, H2O.8 MN.11: 4 residues within 4Å: Chain C: D.190, D.192 Ligands: GTP.10, MN.12 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H2O.5 MN.12: 5 residues within 4Å: Chain C: D.190, D.192, D.256 Ligands: GTP.10, MN.11 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.190, C:D.190, C:D.192, H2O.3, H2O.7

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

NA.6: 1 residues within 4Å: Ligands: GTP.10 No protein-ligand interaction detected (PLIP) NA.7: 5 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, G.105, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.103, C:G.105, C:I.106 NA.8: 4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.60, C:G.64, C:V.65 Water bridges: C:K.60

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 4 residues within 4Å: Chain C: A.32, I.33, H.34, K.35 Ligand excluded by PLIP

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.10: 21 residues within 4Å: Chain A: C.6, G.7 Chain B: C.10 Chain C: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192, G.271, F.272, T.273, G.274, D.276, N.279, R.283 Ligands: NA.6, MN.11, MN.12 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:R.183, C:S.188, C:G.189, C:D.190, C:T.273, C:N.279 Water bridges: C:R.40, C:R.149, C:R.149, C:D.190, C:D.276, C:D.276, C:D.276, C:R.283, C:R.283, C:R.283 Salt bridges: C:R.183

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: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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