SMTL ID : 6dic.1

D276G DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 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.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:K.280 Hydrogen bonds: C:R.40, C:R.283 Water bridges: C:N.37, C:N.37, C:R.40 Salt bridges: C:K.280 pi-Stacking: C:H.34

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

NA.2: 4 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, I.106 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.106, C:I.106 NA.5: 4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.65, C:V.65 Water bridges: C:K.60 NA.9: 1 residues within 4Å: Chain C: R.126 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.126 NA.10: 1 residues within 4Å: Chain C: E.249 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.249 Water bridges: C:Q.240, C:Q.240

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: GKS.4, CA.11 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.190, C:D.192, C:D.256, H2O.9 CA.11: 4 residues within 4Å: Chain C: D.190, D.192 Ligands: CA.3, GKS.4 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.190, C:D.192, H2O.6 CA.12: 1 residues within 4Å: Chain C: D.145 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.145, C:D.145, H2O.5, H2O.10, H2O.13

1 x GKS: 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol(Non-covalent)

GKS.4: 21 residues within 4Å: Chain A: C.6, G.7 Chain B: C.10 Chain C: R.40, G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, S.275, G.276, N.279, R.283 Ligands: CA.3, CA.11 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:R.40, C:S.180, C:S.180, C:S.180, C:R.183, C:G.189, C:D.190, C:D.190, C:D.190, C:N.279 Water bridges: C:Y.36, C:R.40, C:F.181, C:F.181, C:R.183, C:R.183, C:G.276 Salt bridges: C:R.183

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

CL.6: 5 residues within 4Å: Chain C: D.263, Q.264, Y.266, C.267, V.313 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain C: A.32, I.33, H.34, K.35 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain C: N.294, T.297 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, M.R. et al., A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition. Nucleic Acids Res. (2019)

Release Date

2019-01-30

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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