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SMTL ID : 1zjn.1

Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus with dGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 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: E.26, 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.5

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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

Chain C: D.190, D.192
Ligands: DGT.6

3 PLIP interactions:

2 interactions with chain C, 1 Ligand-Water interactions

Metal complexes: C:D.190, C:D.192, H₂O.3

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

NA.3:	5 residues within 4Å: Chain B: A.10 Chain C: D.190, D.192, D.256 Ligands: DGT.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.256
NA.4:	6 residues within 4Å: Chain B: G.9 Chain C: T.101, R.102, 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.5:	6 residues within 4Å: Chain C: K.60, K.61, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 No protein-ligand interaction detected (PLIP)

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.6:

21 residues within 4Å:

Chain A: C.6, A.7
Chain B: A.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, R.283
Ligands: MG.2, NA.3

11 PLIP interactions:

11 interactions with chain C

Hydrogen bonds: C:S.180, C:S.180, C:R.183, C:G.189, C:D.190, C:D.190, C:N.279, C:R.283
Water bridges: C:D.276
Salt bridges: C:R.149, C:R.183

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Batra, V.K. et al., Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. STRUCTURE (2005)

Release Date

2005-08-16

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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