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SMTL ID : 2isp.1

Ternary complex of DNA Polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-methylene triphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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:

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.5

7 PLIP interactions:

7 interactions with chain C

Hydrophobic interactions: C:K.280
Hydrogen bonds: C:R.283
Water bridges: C:R.40, C:K.280, C:K.280
Salt bridges: C:K.280
pi-Stacking: C:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

4 residues within 4Å:

Chain C: D.190, D.192
Ligands: NA.3, GGH.11

3 PLIP interactions:

2 interactions with chain C, 1 Ligand-Water interactions

Metal complexes: C:D.190, C:D.192, H₂O.2

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

NA.3:	6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: MG.2, GGH.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.192
NA.4:	5 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, G.105, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.105, C:I.106, C:I.106
NA.5:	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

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

CL.6:	4 residues within 4Å: Chain C: Q.264, Y.266, C.267, V.313 Ligand excluded by PLIP
CL.7:	4 residues within 4Å: Chain C: A.32, I.33, H.34, K.35 Ligand excluded by PLIP
CL.8:	5 residues within 4Å: Chain C: K.81, L.82, L.85, E.86, R.89 Ligand excluded by PLIP
CL.9:	3 residues within 4Å: Chain C: N.294, T.297, R.299 Ligand excluded by PLIP
CL.10:	3 residues within 4Å: Chain C: E.329, P.330, K.331 Ligand excluded by PLIP

1 x GGH: 2'-DEOXY-5'-O-(HYDROXY{[HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]OXY}PHOSPHORYL)GUANOSINE(Non-covalent)

GGH.11:

21 residues within 4Å:

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

14 PLIP interactions:

14 interactions with chain C

Hydrogen bonds: C:R.149, C:S.180, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:D.190, C:D.192, C:N.279, C:R.283
Water bridges: C:D.276, C:D.276, C:D.276

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sucato, C.A. et al., Modifying the beta,gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase beta. Biochemistry (2007)

Release Date

2007-01-30

Peptides

Polymerase (DNA directed), 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

Polymerase (DNA directed), beta

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