- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.08 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: C.1, C.2, G.3, A.4, C.5
- Chain C: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
- Ligands: NA.6
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:R.283, C:R.283, C:R.283
- pi-Stacking: C:H.34
- 3 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
MG.2: 3 residues within 4Å:- Chain B: C.11
- Ligands: DCP.11, PPV.12
No protein-ligand interaction detected (PLIP)MG.3: 6 residues within 4Å:- Chain B: C.11
- Chain C: D.190, D.192
- Ligands: MG.4, DCP.11, PPV.12
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.190, C:D.192, H2O.4
MG.4: 7 residues within 4Å:- Chain B: G.10, C.11
- Chain C: D.190, D.192, D.256
- Ligands: MG.3, DCP.11
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.190, C:D.192, C:D.256, H2O.2
- 2 x NA: SODIUM ION(Non-functional Binders)
NA.5: 6 residues within 4Å:- Chain B: G.9
- Chain C: T.101, V.103, S.104, G.105, I.106
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:V.103, C:G.105, C:I.106
NA.6: 5 residues within 4Å:- Chain C: K.60, L.62, P.63, V.65
- Ligands: DG-DT-DC-DG-DG.1
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.60, C:V.65
- 4 x CL: CHLORIDE ION(Non-functional Binders)
CL.7: 5 residues within 4Å:- Chain C: D.263, Q.264, Y.266, C.267, V.313
Ligand excluded by PLIPCL.8: 4 residues within 4Å:- Chain C: A.32, I.33, H.34, K.35
Ligand excluded by PLIPCL.9: 3 residues within 4Å:- Chain C: K.81, L.82, E.86
Ligand excluded by PLIPCL.10: 4 residues within 4Å:- Chain C: N.294, Y.296, T.297, R.299
Ligand excluded by PLIP- 1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)
DCP.11: 22 residues within 4Å:- Chain A: G.6
- Chain B: G.10, C.11
- Chain C: R.149, 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
- Ligands: MG.2, MG.3, MG.4, PPV.12
14 PLIP interactions:14 interactions with chain C- Hydrophobic interactions: C:D.276
- Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:S.180, C:R.183, C:G.189, C:D.190, C:D.192, C:N.279
- Water bridges: C:R.149, C:R.149, C:D.276
- Salt bridges: C:R.183
- 1 x PPV: PYROPHOSPHATE(Non-covalent)
PPV.12: 11 residues within 4Å:- Chain B: C.11
- Chain C: G.179, S.180, R.183, S.188, G.189, D.190, D.192
- Ligands: MG.2, MG.3, DCP.11
11 PLIP interactions:11 interactions with chain C- Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:S.180, C:G.189, C:D.190
- Water bridges: C:R.149, C:R.149, C:R.149, C:G.189
- Salt bridges: C:R.183
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Whitaker, A.M. et al., Capturing a mammalian DNA polymerase extending from an oxidized nucleotide. Nucleic Acids Res. (2017)
- Release Date
- 2017-05-10
- Peptides
- DNA polymerase beta: C
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:C
A
SMTL ID : 5v1r.1
DNA polymerase beta reactant complex with 8-oxoG:C at the primer terminus and incoming dCTP
DNA polymerase beta
Related Entries With Identical Sequence
1bpx.1 | 1bpy.1 | 1bpz.1 | 1mq2.1 | 1mq3.1 | 1tv9.1 | 1tva.1 | 1zjm.1 | 1zjn.1 | 1zqa.1 | 1zqb.1 | 1zqc.1 | 1zqd.1 | 1zqe.1 | 1zqf.1 | 1zqg.1 | 1zqh.1 | 1zqi.1 | 1zqj.1 | 1zqk.1 | 1zql.1 | 1zqm.1 | 1zqn.1 | 1zqo.1 | 1zqp.1 | 1zqq.1 | 1zqr.1 | 1zqs.1 | 1zqt.1 | 2fmp.1 more...less...2fmq.1 | 2fms.1 | 2i9g.1 | 2iso.1 | 2isp.1 | 2p66.1 | 2pxi.1 | 3c2k.1 | 3c2l.1 | 3c2m.1 | 3isb.1 | 3isc.1 | 3isd.1 | 3jpn.1 | 3jpo.1 | 3jpp.1 | 3jpq.1 | 3jpr.1 | 3jps.1 | 3jpt.1 | 3lk9.1 | 3mby.1 | 3rh4.1 | 3rje.1 | 3rjf.1 | 3rjg.1 | 3rjh.1 | 3rji.1 | 3rjj.1 | 3rjk.1 | 3tfr.1 | 3tfs.1 | 4do9.1 | 4doa.1 | 4dob.1 | 4doc.1 | 4kld.1 | 4kle.1 | 4klf.1 | 4klg.1 | 4klh.1 | 4kli.1 | 4klj.1 | 4kll.1 | 4klm.1 | 4klo.1 | 4klq.1 | 4kls.1 | 4klt.1 | 4klu.1 | 4lvs.1 | 4o9m.1 | 4rt2.1 | 4rt3.1 | 4uaw.1 | 4uay.1 | 4uaz.1 | 4ub1.1 | 4ub2.1 | 4ub3.1 | 4ub4.1 | 4ub5.1 | 4ubb.1 | 4ubc.1 | 4ymm.1 | 4ymn.1 | 4ymo.1 | 4yn4.1 | 5bol.1 | 5bom.1 | 5bpc.1 | 5db6.1 | 5db7.1 | 5db8.1 | 5db9.1 | 5dba.1 | 5dbb.1 | 5dbc.1 | 5eoz.1 | 5j0o.1 | 5j0p.1 | 5j0q.1 | 5j0r.1 | 5j0s.1 | 5j0t.1 | 5j0u.1 | 5j0w.1 | 5j0x.1 | 5j0y.1 | 5j29.1 | 5j2a.1 | 5j2b.1 | 5j2c.1 | 5j2d.1 | 5j2e.1 | 5j2f.1 | 5j2g.1 | 5j2h.1 | 5j2i.1 | 5j2j.1 | 5j2k.1 | 5tzv.1 | 5u8g.1 | 5u9h.1 | 5ugn.1 | 5ugo.1 | 5ugp.1 | 5v1f.1 | 5v1g.1 | 5v1h.1 | 5v1i.1 | 5v1j.1 | 5v1n.1 | 5v1o.1 | 5v1p.1 | 5vez.1 | 5wnx.1 | 5wny.1 | 5wnz.1 | 5wo0.1 | 6bel.1 | 6bem.1 | 6cly.1 | 6cpq.1 | 6cr4.1 | 6cr5.1 | 6cr6.1 | 6cr7.1 | 6cr8.1 | 6cr9.1 | 6crb.1 | 6crc.1 | 6crh.1 | 6cu9.1 | 6cua.1 | 6cub.1 | 6dia.1 | 6e3r.1 | 6e3v.1 | 6e3w.1 | 6e3x.1 | 6g2q.1 | 6mr7.1 | 6n2r.1 | 6n2s.1 | 6n2t.1 | 6nku.1 | 6nkv.1 | 6nkw.1 | 6ph5.1 | 6ph6.1 | 6u2o.1 | 6u6b.1 | 6w2m.1 | 7ice.1 | 7icf.1 | 7icg.1 | 7ich.1 | 7ici.1 | 7icj.1 | 7ick.1 | 7icl.1 | 7icm.1 | 7icn.1 | 7ico.1 | 7icp.1 | 7icq.1 | 7icr.1 | 7ics.1 | 7ict.1 | 7icu.1 | 7icv.1 | 7k96.1 | 7s9j.1 | 7s9k.1 | 7s9l.1 | 7s9m.1 | 7s9n.1 | 7s9o.1 | 7s9p.1 | 7s9q.1 | 8ica.1 | 8icb.1 | 8icc.1 | 8ice.1 | 8icf.1 | 8icg.1 | 8ich.1 | 8ici.1 | 8icj.1 | 8ick.1 | 8icl.1 | 8icm.1 | 8icn.1 | 8ico.1 | 8icp.1 | 8icq.1 | 8icr.1 | 8ics.1 | 8ict.1 | 8icu.1 | 8icv.1 | 8icw.1 | 8icx.1 | 8icy.1 | 8icz.1 | 8vf8.1 | 8vf9.1 | 8vfa.1 | 8vfb.1 | 8vfc.1 | 8vfd.1 | 8vfe.1 | 8vff.1 | 8vfg.1 | 8vfh.1 | 8vfi.1 | 8vfj.1 | 9dwg.1 | 9dwh.1 | 9dwi.1 | 9dwk.1 | 9dwm.1 | 9ica.1 | 9icb.1 | 9icc.1 | 9ice.1 | 9icf.1 | 9icg.1 | 9ich.1 | 9ici.1 | 9icj.1 | 9ick.1 | 9icl.1 | 9icm.1 | 9icn.1 | 9ico.1 | 9icp.1 | 9icq.1 | 9icr.1 | 9ics.1 | 9ict.1 | 9icu.1 | 9icv.1 | 9icw.1 | 9icx.1 | 9icy.1