3c2l.1 | SWISS-MODEL Template Library

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SMTL ID : 3c2l.1

Ternary complex of DNA POLYMERASE BETA with a C:DAPCPP mismatch in the active site

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*DGP*DTP*DCP*DGP*DG)-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.9

4 PLIP interactions:

4 interactions with chain C

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

6 x MN: MANGANESE (II) ION(Non-functional Binders)(Non-covalent)

MN.2:	1 residues within 4Å: Chain A: G.3 No protein-ligand interaction detected (PLIP)
MN.3:	1 residues within 4Å: Chain B: G.4 No protein-ligand interaction detected (PLIP)
MN.4:	4 residues within 4Å: Chain C: D.190, D.192 Ligands: MN.5, F2A.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H₂O.4
MN.5:	5 residues within 4Å: Chain C: D.190, D.192, D.256 Ligands: MN.4, F2A.10 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, C:D.256, H₂O.2, H₂O.2
MN.6:	1 residues within 4Å: Chain C: D.124 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.124, H₂O.4, H₂O.4
MN.7:	1 residues within 4Å: Chain C: H.51 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.51

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

NA.8:	6 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, G.105, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.103, C:G.105, C:I.106
NA.9:	5 residues within 4Å: Chain C: K.60, K.61, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.60

1 x F2A: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine(Non-covalent)

F2A.10:

20 residues within 4Å:

Chain A: C.6
Chain B: C.10
Chain C: 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, K.280
Ligands: MN.4, MN.5

12 PLIP interactions:

12 interactions with chain C

Hydrogen bonds: C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:Y.271, C:D.276, C:N.279, C:K.280
Water bridges: C:K.280
Salt bridges: C:R.149

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Batra, V.K. et al., Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Mol.Cell (2008)

Release Date

2008-05-20

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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