6ph6.1 | SWISS-MODEL Template Library

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SMTL ID : 6ph6.1

Ternary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstream

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x DG- DC- DT- DG- DA- DT- DG- DC- DG: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*G)-3')(Non-covalent)

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

19 residues within 4Å:

Chain A: V.103, S.104, G.105, I.106, G.107, P.108, S.109, A.110, R.254
Chain B: C.8, G.9, C.10, A.11, T.12, C.13, A.14, G.15, C.16
Ligands: NA.6

Protein-ligand interaction information (PLIP) not available

1 x DG- DT- DC- DG- DG: DNA (5'-D(P*GP*TP*CP*GP*G)-3')(Non-covalent)

DG-DT-DC-DG-DG.2:

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.7

Protein-ligand interaction information (PLIP) not available

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

DCP.3:

19 residues within 4Å:

Chain A: 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
Chain B: G.6, G.7
Ligands: MG.4, MG.5

11 PLIP interactions:

11 interactions with chain A

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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4:	4 residues within 4Å: Chain A: S.180, D.190, D.192 Ligands: DCP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.190, A:D.192
MG.5:	4 residues within 4Å: Chain A: D.190, D.192, D.256 Ligands: DCP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.190, A:D.192, A:D.256

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

NA.6:	6 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, I.106 Ligands: DG-DC-DT-DG-DA-DT-DG-DC-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106
NA.7:	2 residues within 4Å: Chain A: P.63 Ligands: DG-DT-DC-DG-DG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.62 Water bridges: A:V.65

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Howard, M.J. et al., DNA polymerase beta nucleotide-stabilized template misalignment fidelity depends on local sequence context. J.Biol.Chem. (2020)

Release Date

2019-12-11

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

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