SMTL ID : 4rpz.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 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.36, K.37, A.40, Y.41, L.64, G.66, V.67, G.68, T.69, K.70, I.71, K.74 Chain C: C.2, G.3, A.4, C.5 Ligands: NA.4, DCP.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.282, A:R.285 pi-Stacking: A:H.36

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, C.11 Ligands: MG.3, DCP.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.192, A:D.192, A:D.194, A:D.258 MG.3: 6 residues within 4Å: Chain A: D.192, D.194 Chain B: C.11 Ligands: MG.2, PPV.10, DCP.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.194, H2O.5 MG.14: 3 residues within 4Å: Chain B: C.11 Ligands: PPV.10, DCP.11 No protein-ligand interaction detected (PLIP)

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

NA.4: 4 residues within 4Å: Chain A: K.62, L.64, V.67 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.67 NA.5: 6 residues within 4Å: Chain A: T.103, V.105, S.106, G.107, 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.6: 2 residues within 4Å: Chain A: D.320, D.323 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.320 NA.13: 1 residues within 4Å: Ligands: DCP.12 No protein-ligand interaction detected (PLIP)

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

CL.7: 3 residues within 4Å: Chain A: Q.266, Y.268, C.269 Ligand excluded by PLIP 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: A.34, I.35, H.36, K.37 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: C.11 Ligands: MG.3, DCP.11, MG.14 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:S.182, A:G.191, A:D.192 Salt bridges: A:R.151, A:R.185

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

DCP.11: 23 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, S.277, D.278, N.281 Chain B: C.10, C.11 Chain C: G.6, G.7 Ligands: MG.2, MG.3, PPV.10, MG.14 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.278 Hydrogen bonds: A:S.182, A:S.182, A:R.185, A:G.191, A:D.192, A:D.192, A:D.192, A:N.281 Salt bridges: A:R.151, A:R.185 DCP.12: 4 residues within 4Å: Chain C: C.2 Ligands: DG-DT-DC-DG-DG.1, DG-DT-DC-DG-DG.1, NA.13 No protein-ligand interaction detected (PLIP)

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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