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SMTL ID : 4doc.1

Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: G T C G G(Non-covalent)

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

19 residues within 4Å:

Chain A: 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
Chain B: C.1, C.2, G.3, A.4, C.5
Ligands: NA.5

6 PLIP interactions:

6 interactions with chain A

Hydrophobic interactions: A:K.280
Hydrogen bonds: A:R.283
Water bridges: A:N.37, A:R.40
Salt bridges: A:K.280
pi-Stacking: A:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

4 residues within 4Å:

Chain A: D.190, D.192
Ligands: NA.3, G1C.11

3 PLIP interactions:

2 interactions with chain A, 1 Ligand-Water interactions

Metal complexes: A:D.190, A:D.192, H₂O.1

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

NA.3:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: C.10 Ligands: MG.2, G1C.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.256
NA.4:	4 residues within 4Å: Chain A: T.101, V.103, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106
NA.5:	5 residues within 4Å: Chain A: K.60, K.61, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.61, A:V.65 Water bridges: A:K.60

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

CL.6:	6 residues within 4Å: Chain A: D.263, Q.264, Y.265, Y.266, C.267, V.313 Ligand excluded by PLIP
CL.7:	4 residues within 4Å: Chain A: A.32, I.33, H.34, K.35 Ligand excluded by PLIP
CL.8:	5 residues within 4Å: Chain A: K.81, L.82, L.85, E.86, R.89 Ligand excluded by PLIP
CL.9:	4 residues within 4Å: Chain A: N.294, Y.296, T.297, R.299 Ligand excluded by PLIP
CL.10:	3 residues within 4Å: Chain A: E.329, P.330, K.331 Ligand excluded by PLIP

1 x G1C: 5'-O-[(R)-{[(S)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine(Non-covalent)

G1C.11:

20 residues within 4Å:

Chain A: 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
Chain B: C.6, G.7
Chain C: C.10
Ligands: MG.2, NA.3

11 PLIP interactions:

11 interactions with chain A

Hydrogen bonds: A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:N.279, A:R.283
Water bridges: A:R.40, A:R.149, A:D.190, A:D.276

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Wu, Y. et al., Beta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases. J.Am.Chem.Soc. (2012)

Release Date

2012-06-13

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
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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