SMTL ID : 6mr7.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 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: 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.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.37, A:N.37 pi-Stacking: A:H.34

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.2: 20 residues within 4Å: Chain A: G.179, S.180, R.183, S.188, G.189, D.190, D.192, R.258, Y.271, F.272, G.274, S.275, D.276, N.279 Chain B: A.6, G.7 Chain C: C.10 Ligands: CA.3, NA.7, EDO.10 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.149, A:S.180, A:G.189, A:D.190, A:R.258, A:R.258, A:Y.271 Water bridges: A:G.179, A:S.180, A:S.180, A:D.190, A:D.190, A:D.192, A:D.192, A:D.192, A:D.256, A:D.256 Salt bridges: A:R.183, A:D.192 pi-Stacking: A:F.272

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: GKS.2, NA.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.1, H2O.4 CA.4: 1 residues within 4Å: Chain A: D.145 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.2, H2O.6, H2O.6, H2O.7, H2O.7

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

NA.5: 4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.60, A:V.65 NA.6: 6 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106 NA.7: 4 residues within 4Å: Chain A: D.190 Ligands: GKS.2, CA.3, EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.190 NA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.8: 4 residues within 4Å: Chain A: P.312, D.314, D.318 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.312, A:D.314 EDO.9: 3 residues within 4Å: Chain A: D.314, D.318 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.315, A:D.318 EDO.10: 5 residues within 4Å: Chain A: Y.271, E.295, Y.296 Chain B: C.8 Ligands: GKS.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.258, A:Y.271, A:Y.271, A:E.295, A:Y.296, A:Y.296 Water bridges: A:R.258 EDO.11: 4 residues within 4Å: Chain A: F.146, K.148, G.189 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.148 Water bridges: A:D.190

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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