SMTL ID : 4rpy.1

Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dCTP soaked with MgCl2 for 30 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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, P.65, G.66, V.67, G.68, T.69, K.70, I.71 Chain C: C.2, G.3, A.4, C.5 Ligands: NA.5, DCP.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.282, A:R.285 Water bridges: A:H.36 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.15 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.192, A:D.194, A:D.258, H2O.9 MG.3: 6 residues within 4Å: Chain A: D.192, D.194 Chain B: C.11 Ligands: MG.2, PPV.14, DCP.15 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.194, H2O.1 MG.17: 3 residues within 4Å: Chain B: C.11 Ligands: PPV.14, DCP.15 No protein-ligand interaction detected (PLIP)

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

NA.4: 2 residues within 4Å: Chain A: E.251, H.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.251 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:V.67, A:V.67 NA.6: 1 residues within 4Å: Chain A: D.162 No protein-ligand interaction detected (PLIP) NA.7: 3 residues within 4Å: Chain A: K.319, D.320, D.323 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.323 NA.8: 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.16: 1 residues within 4Å: Ligands: DCP.18 No protein-ligand interaction detected (PLIP) NA.19: 1 residues within 4Å: Chain C: A.11 No protein-ligand interaction detected (PLIP)

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

CL.9: 3 residues within 4Å: Chain A: N.135, H.136, H.137 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: D.265, Q.266, Y.267, Y.268, C.269, V.315 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: N.296, Y.298, T.299, R.301 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: A.34, I.35, H.36, K.37 Ligand excluded by PLIP

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

ACT.13: 6 residues within 4Å: Chain A: N.39, R.42, D.278, I.279, K.282 Chain C: G.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.278 Salt bridges: A:R.42 ACT.20: 5 residues within 4Å: Chain B: T.6, G.7, C.8 Chain C: C.8, G.9 No protein-ligand interaction detected (PLIP)

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.14: 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.15, MG.17 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

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

DCP.15: 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, S.277, D.278, N.281 Chain B: C.10, C.11 Chain C: G.6 Ligands: MG.2, MG.3, PPV.14, MG.17 12 PLIP interactions: 12 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:N.281 Water bridges: A:D.192, A:D.258, A:D.278 Salt bridges: A:R.151, A:R.185 DCP.18: 4 residues within 4Å: Chain C: C.2 Ligands: DG-DT-DC-DG-DG.1, DG-DT-DC-DG-DG.1, NA.16 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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