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SMTL ID : 1bpy.1

HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

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

19 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, K.41, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Ligands: NA.5

5 PLIP interactions:

5 interactions with chain C

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

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

NA.4:	5 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, I.106 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.106, C:I.106
NA.5:	5 residues within 4Å: Chain C: K.60, L.62, G.64, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.62, C:G.64 Water bridges: C:K.60

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.6:

18 residues within 4Å:

Chain A: G.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: MG.2, MG.3

13 PLIP interactions:

13 interactions with chain C

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sawaya, M.R. et al., Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry (1997)

Release Date

1997-06-16

Peptides

PROTEIN (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

PROTEIN (DNA POLYMERASE BETA)

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