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SMTL ID : 4kle.1

DNA polymerase beta matched reactant complex with Mg2+, 10 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: 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

5 PLIP interactions:

5 interactions with chain C

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

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

DCP.2:

22 residues within 4Å:

Chain A: G.6, G.7
Chain B: C.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.3, MG.4, PPV.5

15 PLIP interactions:

15 interactions with chain C

Hydrophobic interactions: C:D.276
Hydrogen bonds: C:S.180, C:S.180, C:R.183, C:G.189, C:D.190, C:D.192, C:N.279
Water bridges: C:S.180, C:R.183, C:R.183, C:D.190, C:D.276
Salt bridges: C:R.149, C:R.183

2 x MG: MAGNESIUM ION(Non-covalent)

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

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.5:

11 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: DCP.2, MG.4

7 PLIP interactions:

7 interactions with chain C

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Freudenthal, B.D. et al., Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.) (2013)

Release Date

2013-07-17

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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