5ugo.1 | SWISS-MODEL Template Library

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SMTL ID : 5ugo.1

DNA polymerase beta nick complex with imidodiphosphate

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:

17 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

6 PLIP interactions:

6 interactions with chain C

Hydrogen bonds: C:H.34, C:R.283, C:R.283
Water bridges: C:N.37
Salt bridges: C:K.280
pi-Stacking: C:H.34

1 x 2PN: IMIDODIPHOSPHORIC ACID(Non-covalent)

2PN.2:

10 residues within 4Å:

Chain B: C.11
Chain C: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192
Ligands: CA.3

9 PLIP interactions:

9 interactions with chain C

Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190
Water bridges: C:F.181

2 x CA: CALCIUM ION(Non-covalent)

CA.3:	5 residues within 4Å: Chain B: C.11 Chain C: D.190, D.192 Ligands: 2PN.2, CA.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H₂O.10
CA.4:	6 residues within 4Å: Chain B: C.10, C.11 Chain C: D.190, D.192, D.256 Ligands: CA.3 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.7

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Shock, D.D. et al., Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction. Nat. Chem. Biol. (2017)

Release Date

2017-07-26

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

DNA polymerase beta

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