SMTL ID : 3tfr.1

Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CF2)PP in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: DNA (5'-D(P*GP*TP*CP*GP*G)-3')(Non-covalent)

DG-DT-DC-DG-DG.1: 18 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 Chain B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.280 Hydrogen bonds: A:R.283 Water bridges: A:H.34, A:N.37, A:R.40, A:K.280, A:K.280 Salt bridges: A:K.280 pi-Stacking: A:H.34

1 x F3A: 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine(Non-covalent)

F3A.2: 20 residues within 4Å: Chain A: 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 Chain B: T.6, G.7 Chain C: C.10 Ligands: MG.3, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.190, A:D.190, A:N.279 Water bridges: A:R.40, A:R.149, A:S.180, A:D.276, A:D.276, A:D.276

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: F3A.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H2O.1 MG.4: 6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: C.10 Ligands: F3A.2, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.190, A:D.192, A:D.256

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

NA.5: 5 residues within 4Å: Chain A: T.101, V.103, S.104, 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.6: 4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.60, A:V.65 Water bridges: A:K.60

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chamberlain, B.T. et al., Stereospecific Formation of a Ternary Complex of (S)-alpha, beta-Fluoromethylene-dATP with DNA Pol beta. Chembiochem (2012)

Release Date

2012-03-21

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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