SMTL ID : 4m9l.1

DNA Polymerase Beta E295K Soaked with dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: DNA Downstream Strand(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.3 7 PLIP interactions: 7 interactions with chain A Water bridges: A:N.37, A:R.283, A:R.283 Salt bridges: A:R.283 pi-Stacking: A:H.34 pi-Cation interactions: A:R.283, A:R.283

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

NA.2: 4 residues within 4Å: Chain A: T.101, V.103, I.106 Chain C: G.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.103, A:I.106 NA.3: 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.4: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: MG.5, DCP.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.192 Water bridges: A:M.191

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.6: 18 residues within 4Å: Chain A: 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.6 Chain C: C.10 Ligands: NA.4, MG.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:D.276 Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:G.189, A:D.190, A:D.190, A:N.279 Water bridges: A:R.149, A:R.149, A:R.149, A:R.183, A:R.183, A:Y.271, A:D.276, A:D.276, A:D.276, A:R.283 Salt bridges: A:R.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eckenroth, B.E. et al., The E295K Cancer Variant of Human Polymerase beta Favors the Mismatch Conformational Pathway during Nucleotide Selection. J.Biol.Chem. (2013)

Release Date

2013-10-16

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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