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SMTL ID : 1tva.1

HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE THYMIDINE AND INCOMING CYTIDINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: 5'-D(P*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, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69, K.72
Ligands: NA.4

2 PLIP interactions:

2 interactions with chain C

Water bridges: C:H.34
pi-Stacking: C:H.34

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2:	4 residues within 4Å: Chain B: C.10, C.11 Chain C: D.190, D.192 No protein-ligand interaction detected (PLIP)
MG.6:	1 residues within 4Å: Chain C: S.30 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.30, H₂O.4, H₂O.4

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

NA.3:	5 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.105, C:I.106, C:I.106
NA.4:	4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.60, C:V.65

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5:

4 residues within 4Å:

Chain C: S.180, S.188, G.189, D.190

4 PLIP interactions:

4 interactions with chain C

Hydrogen bonds: C:S.180, C:S.180, C:G.189, C:D.190

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Krahn, J.M. et al., Structural insights into DNA polymerase Beta deterrents for misincorporation support an induced-fit mechanism for fidelity. Structure (2004)

Release Date

2004-11-23

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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