- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 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: K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
- Ligands: NA.9, EDO.20
7 PLIP interactions:7 interactions with chain C- Hydrophobic interactions: C:K.280
- Hydrogen bonds: C:R.283
- Water bridges: C:N.37, C:N.37, C:N.37
- Salt bridges: C:K.280
- pi-Stacking: C:H.34
- 9 x CL: CHLORIDE ION(Non-functional Binders)
CL.2: 2 residues within 4Å:- Chain A: A.4, C.5
Ligand excluded by PLIPCL.11: 4 residues within 4Å:- Chain C: N.294, T.297, R.299
- Ligands: EDO.22
Ligand excluded by PLIPCL.12: 4 residues within 4Å:- Chain C: A.32, I.33, H.34, K.35
Ligand excluded by PLIPCL.13: 1 residues within 4Å:- Chain C: R.89
Ligand excluded by PLIPCL.14: 1 residues within 4Å:- Chain C: K.127
Ligand excluded by PLIPCL.15: 5 residues within 4Å:- Chain C: Q.219, T.225, D.226, T.227
- Ligands: CL.16
Ligand excluded by PLIPCL.16: 4 residues within 4Å:- Chain C: H.134, D.226, T.227
- Ligands: CL.15
Ligand excluded by PLIPCL.17: 2 residues within 4Å:- Chain C: K.148, R.149
Ligand excluded by PLIPCL.18: 3 residues within 4Å:- Chain A: C.10
- Chain C: G.231, E.232
Ligand excluded by PLIP- 4 x NA: SODIUM ION(Non-functional Binders)
NA.3: 3 residues within 4Å:- Chain A: G.9
- Chain B: G.7, C.8
No protein-ligand interaction detected (PLIP)NA.8: 5 residues within 4Å:- Chain B: G.9
- Chain C: T.101, V.103, G.105, I.106
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:V.103, C:G.105, C:I.106
NA.9: 4 residues within 4Å:- Chain C: K.60, L.62, V.65
- Ligands: DG-DT-DC-DG-DG.1
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:V.65, C:V.65
NA.10: 3 residues within 4Å:- Chain C: Q.90, D.91, D.92
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:D.92
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.4: 3 residues within 4Å:- Chain C: R.83, K.84, K.87
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:R.83, C:R.83, C:K.84
EDO.20: 7 residues within 4Å:- Chain A: C.5
- Chain C: H.34, N.37, A.38, K.41, K.280
- Ligands: DG-DT-DC-DG-DG.1
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:H.34, C:K.41, C:K.280
EDO.21: 3 residues within 4Å:- Chain C: K.168, Q.217, V.221
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:K.168, C:Q.217, C:Q.217
EDO.22: 5 residues within 4Å:- Chain C: Q.264, Y.296, T.297, R.299
- Ligands: CL.11
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Q.264, C:R.299
- 3 x CA: CALCIUM ION(Non-covalent)
CA.5: 4 residues within 4Å:- Chain C: D.190, D.192
- Ligands: CA.6, DGI.19
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.190, C:D.190, C:D.192, H2O.3, H2O.3
CA.6: 6 residues within 4Å:- Chain B: C.10
- Chain C: D.190, D.192, D.256
- Ligands: CA.5, DGI.19
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.190, C:D.190, C:D.192, C:D.256, H2O.4
CA.7: 1 residues within 4Å:- Chain C: D.276
4 PLIP interactions:1 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: C:D.276, H2O.4, H2O.5, H2O.6
- 1 x DGI: 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE(Non-covalent)
DGI.19: 17 residues within 4Å:- Chain A: C.6, G.7
- Chain B: C.10
- Chain C: G.179, S.180, R.183, D.190, D.192, Y.271, F.272, T.273, G.274, D.276, N.279, R.283
- Ligands: CA.5, CA.6
13 PLIP interactions:13 interactions with chain C- Hydrogen bonds: C:S.180, C:S.180, C:R.183, C:N.279, C:R.283
- Water bridges: C:S.180, C:G.189, C:G.189, C:D.190, C:D.276, C:D.276, C:D.276
- Salt bridges: C:R.183
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Varela, F.A. et al., Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase beta. Biochemistry (2021)
- Release Date
- 2021-02-03
- Peptides
- DNA polymerase beta: C
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:C
A
SMTL ID : 7k96.1
Human DNA polymerase beta ternary complex with templating cytosine and incoming deoxyguanosine diphosphate
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 | 5v1r.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 | 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 | 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