SMTL ID : 3uxp.1 (1 other biounit)

Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

monomer

Ligands

1 x DA- DT- DG- DT- DG- DA- DG: DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3'(Non-covalent)

DA-DT-DG-DT-DG-DA-DG.1: 23 residues within 4Å: Chain A: V.103, T.104, G.105, I.106, G.107, P.108, S.109, A.110, D.190, K.234, R.254, Y.271 Ligands: DA-DC-DT-DC-DA-DC-DA-DT-DA.2, DA-DC-DT-DC-DA-DC-DA-DT-DA.2, DA-DC-DT-DC-DA-DC-DA-DT-DA.2, DA-DC-DT-DC-DA-DC-DA-DT-DA.2, DA-DC-DT-DC-DA-DC-DA-DT-DA.2, DA-DC-DT-DC-DA-DC-DA-DT-DA.2, DA-DC-DT-DC-DA-DC-DA-DT-DA.2, DA-DC-DT-DC-DA-DC-DA-DT-DA.2, D3T.3, NA.4, NA.6 Protein-ligand interaction information (PLIP) not available

1 x DA- DC- DT- DC- DA- DC- DA- DT- DA: DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3'(Non-covalent)

DA-DC-DT-DC-DA-DC-DA-DT-DA.2: 25 residues within 4Å: Chain A: S.229, K.230, G.231, E.232, T.233, K.234, R.258, K.280, R.283, A.284, L.287, T.292, I.293, N.294, E.295, Y.296 Ligands: DA-DT-DG-DT-DG-DA-DG.1, DA-DT-DG-DT-DG-DA-DG.1, DA-DT-DG-DT-DG-DA-DG.1, DA-DT-DG-DT-DG-DA-DG.1, DA-DT-DG-DT-DG-DA-DG.1, DA-DT-DG-DT-DG-DA-DG.1, DA-DT-DG-DT-DG-DA-DG.1, D3T.3, NA.7 Protein-ligand interaction information (PLIP) not available

1 x D3T: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

D3T.3: 17 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, G.274, D.276, N.279 Ligands: DA-DT-DG-DT-DG-DA-DG.1, DA-DC-DT-DC-DA-DC-DA-DT-DA.2, NA.4, NA.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.276 Hydrogen bonds: A:S.180, A:S.180, A:G.189, A:D.190, A:D.190, A:D.276, A:N.279 Water bridges: A:D.276, A:D.276 Salt bridges: A:R.149, A:R.183

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

NA.4: 5 residues within 4Å: Chain A: D.190, D.192, D.256 Ligands: DA-DT-DG-DT-DG-DA-DG.1, D3T.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192 NA.5: 3 residues within 4Å: Chain A: D.190, D.192 Ligands: D3T.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.190, A:D.190 NA.6: 5 residues within 4Å: Chain A: T.101, V.103, T.104, I.106 Ligands: DA-DT-DG-DT-DG-DA-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106 NA.7: 7 residues within 4Å: Chain A: R.283, L.287, F.291, T.292, I.293 Ligands: DA-DC-DT-DC-DA-DC-DA-DT-DA.2, DA-DC-DT-DC-DA-DC-DA-DT-DA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.291, A:I.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gridley, C.L. et al., Structural Changes in the Hydrophobic Hinge Region Adversely Affect the Activity and Fidelity of the I260Q Mutator DNA Polymerase beta. Biochemistry (2013)

Release Date

2012-12-05

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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