SMTL ID : 4rq5.1

Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dATP soaked with MgCl2 for 60 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 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: 19 residues within 4Å: Chain A: H.36, K.37, A.40, Y.41, L.64, P.65, G.66, V.67, G.68, T.69, K.70, I.71, K.74 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: NA.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.36, A:K.282, A:R.285

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 7 residues within 4Å: Chain A: D.192, D.194, D.258 Chain B: C.10, A.11 Ligands: MG.3, DTP.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.194, A:D.258, H2O.2 MG.3: 6 residues within 4Å: Chain A: D.192, D.194 Chain B: A.11 Ligands: MG.2, PPV.10, DTP.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.194, H2O.2 MG.12: 3 residues within 4Å: Chain B: A.11 Ligands: PPV.10, DTP.11 No protein-ligand interaction detected (PLIP)

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

NA.4: 4 residues within 4Å: Chain A: T.103, V.105, I.108 Chain B: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.107, A:I.108, A:I.108 NA.5: 4 residues within 4Å: Chain A: K.62, L.64, V.67 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.64, A:V.67

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 1 residues within 4Å: Chain A: N.135 No protein-ligand interaction detected (PLIP) ACT.7: 3 residues within 4Å: Chain A: F.202, T.207, E.234 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.202 Hydrogen bonds: A:E.234

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

CL.8: 4 residues within 4Å: Chain A: N.296, Y.298, T.299, R.301 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: Q.266, Y.267, Y.268, C.269 Ligand excluded by PLIP

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.10: 12 residues within 4Å: Chain A: R.151, G.181, S.182, R.185, S.190, G.191, D.192, D.194 Chain B: A.11 Ligands: MG.3, DTP.11, MG.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:G.191, A:D.192 Salt bridges: A:R.151, A:R.185

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.11: 22 residues within 4Å: Chain A: R.151, G.181, S.182, R.185, S.190, G.191, D.192, D.194, Y.273, F.274, T.275, G.276, D.278, N.281 Chain B: C.10, A.11 Chain C: G.6, G.7 Ligands: MG.2, MG.3, PPV.10, MG.12 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:R.185, A:G.191, A:D.192, A:D.192, A:N.281 Water bridges: A:D.278, A:D.278 Salt bridges: A:R.151, A:R.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vyas, R. et al., Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography. J.Am.Chem.Soc. (2015)

Release Date

2015-04-15

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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