6n2t.1 | SWISS-MODEL Template Library

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SMTL ID : 6n2t.1

Ternary complex crystal structure of DNA polymerase Beta with 5-hydroxymethyl-dC (5-hmC) at the templating position

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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: 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

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:R.283

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: MG.3, 1GC.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.2
MG.3:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: C.10 Ligands: MG.2, 1GC.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H₂O.2

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

NA.4:	6 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106
NA.5:	4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 No protein-ligand interaction detected (PLIP)

1 x 1GC: 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine(Non-covalent)

1GC.6:

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

10 PLIP interactions:

10 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:N.279, A:R.283
Water bridges: A:F.181
Salt bridges: A:R.149

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Howard, M.J. et al., Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta. J.Biol.Chem. (2019)

Release Date

2019-03-27

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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