4dob.1 | SWISS-MODEL Template Library

Modelling
Repository
Tools
Documentation
Log in
Create Account

SMTL ID : 4dob.1

Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate: Stereoselective binding of R-isomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: G T C G G(Non-covalent)

DG-DT-DC-DG-DG.1:

18 residues within 4Å:

Chain A: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Chain B: C.1, C.2, G.3, A.4, C.5
Ligands: NA.5

6 PLIP interactions:

6 interactions with chain A

Hydrophobic interactions: A:K.280
Hydrogen bonds: A:R.283
Water bridges: A:R.40, A:R.40
Salt bridges: A:K.280
pi-Stacking: A:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

4 residues within 4Å:

Chain A: D.190, D.192
Ligands: NA.3, GRC.11

3 PLIP interactions:

2 interactions with chain A, 1 Ligand-Water interactions

Metal complexes: A:D.190, A:D.192, H₂O.6

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

NA.3:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: C.10 Ligands: MG.2, GRC.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192
NA.4:	4 residues within 4Å: Chain A: T.101, V.103, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106
NA.5:	5 residues within 4Å: Chain A: K.60, K.61, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.61, A:V.65

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

CL.6:	5 residues within 4Å: Chain A: D.263, Q.264, Y.266, C.267, V.313 Ligand excluded by PLIP
CL.7:	4 residues within 4Å: Chain A: A.32, I.33, H.34, K.35 Ligand excluded by PLIP
CL.8:	3 residues within 4Å: Chain A: K.81, L.82, R.89 Ligand excluded by PLIP
CL.9:	4 residues within 4Å: Chain A: N.294, Y.296, T.297, R.299 Ligand excluded by PLIP
CL.10:	3 residues within 4Å: Chain A: E.329, P.330, K.331 Ligand excluded by PLIP

1 x GRC: 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine(Non-covalent)

GRC.11:

20 residues within 4Å:

Chain A: 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, R.283
Chain B: C.6, G.7
Chain C: C.10
Ligands: MG.2, NA.3

16 PLIP interactions:

16 interactions with chain A

Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.192, A:N.279, A:R.283
Water bridges: A:R.149, A:R.149, A:D.190, A:D.276, A:D.276, A:D.276, A:D.276

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Wu, Y. et al., Beta,Gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases. J.Am.Chem.Soc. (2012)

Release Date

2012-06-13

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

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 | 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 | 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 | 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

Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

Swiss Institute of BioinformaticsSIB
Schwede Group
Contact Us
Terms of use
Back to the Top