SMTL ID : 6btf.1

DNA Polymerase Beta I260Q Ternary Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: DNA Downstream Strand(Non-covalent)

DG-DT-DC-DG-DG.1: 16 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: G.1, A.2, C.3 Ligands: NA.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.283 Water bridges: A:N.37 Salt bridges: A:K.280 pi-Stacking: A:H.34

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

NA.2: 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.3: 4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.62, A:V.65 Water bridges: A:K.60 NA.5: 6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: C.10 Ligands: MG.4, DUP.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.190

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.6: 19 residues within 4Å: Chain A: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, S.275, D.276, N.279 Chain B: A.4 Chain C: C.10 Ligands: MG.4, NA.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.276 Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.192, A:N.279 Water bridges: A:F.181, A:F.181, A:D.190, A:D.276, A:D.276 Salt bridges: A:R.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liptak, C. et al., I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity. Nucleic Acids Res. (2018)

Release Date

2018-09-26

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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