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SMTL ID : 6u2o.1

Structure of human DNA polymerase beta misinserting dAMPNPP opposite the 5'G of the cisplatin Pt-GG intrastrand crosslink

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

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

19 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, K.72
Chain B: C.1, C.2, C.3, A.4, C.5
Ligands: NA.6

5 PLIP interactions:

5 interactions with chain A

Hydrogen bonds: A:N.37, A:K.280, A:K.280, A:K.280
pi-Stacking: A:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

Chain A: D.190, D.192
Ligands: DZ4.4

3 PLIP interactions:

2 interactions with chain A, 1 Ligand-Water interactions

Metal complexes: A:D.190, A:D.192, H₂O.1

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

NA.3:	5 residues within 4Å: Chain A: T.101, V.103, 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.6:	4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DG-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.62

1 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.4:

16 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, D.276, N.279
Chain B: G.7
Chain C: C.10
Ligands: MG.2

15 PLIP interactions:

15 interactions with chain A

Hydrophobic interactions: A:D.276
Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:Y.271
Water bridges: A:R.149, A:R.149, A:D.190, A:D.190, A:N.279
pi-Stacking: A:Y.271

1 x CPT: Cisplatin(Non-functional Binders)

CPT.5:

2 residues within 4Å:

Chain B: G.6, G.7

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Ouzon-Shubeita, H. et al., Structures of the Mutagenic Bypass of the Major Cisplatin-DNA Lesion by Human DNA Polymerase Beta Reveal Insights into Cisplatin-Induced Mutagenesis. To Be Published

Release Date

2020-08-26

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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