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SMTL ID : 5wo0.1

DNA polymerase beta substrate complex with incoming 5-FodUTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: 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
Ligands: NA.4

4 PLIP interactions:

4 interactions with chain C

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

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

NA.2:	4 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.105, C:I.106, C:I.106
NA.4:	6 residues within 4Å: Chain C: K.60, K.61, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.62, C:V.65

2 x CA: CALCIUM ION(Non-covalent)

CA.3:	6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: B7A.8, CA.9 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.6
CA.9:	4 residues within 4Å: Chain C: D.190, D.192 Ligands: CA.3, B7A.8 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.190, C:D.192, H₂O.6

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5:	4 residues within 4Å: Chain C: A.32, I.33, H.34, K.35 Ligand excluded by PLIP
CL.6:	4 residues within 4Å: Chain C: K.81, L.82, L.85, E.86 Ligand excluded by PLIP
CL.7:	2 residues within 4Å: Chain C: N.294, T.297 Ligand excluded by PLIP

1 x B7A: 2'-deoxy-5-formyluridine 5'-(tetrahydrogen triphosphate)(Non-covalent)

B7A.8:

18 residues within 4Å:

Chain A: A.6
Chain B: C.10
Chain C: 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: CA.3, CA.9

16 PLIP interactions:

16 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.190, C:D.192, C:N.279
Water bridges: C:F.181, C:F.181, C:R.183, C:R.183, C:D.190, C:D.276
Salt bridges: C:R.183

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Schaich, M.A. et al., Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues. Chem. Res. Toxicol. (2017)

Release Date

2017-09-13

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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