SMTL ID : 3gdx.1

Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP

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: H.25, K.26, A.29, Y.30, L.53, P.54, G.55, V.56, G.57, T.58, K.59, I.60 Chain B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.25, A:K.271, A:K.271, A:R.274 Water bridges: A:R.31 Salt bridges: A:K.271 pi-Stacking: A:H.25

1 x 4BD: 5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine(Non-covalent)

4BD.2: 19 residues within 4Å: Chain A: R.140, G.170, S.171, R.174, S.179, G.180, D.181, D.183, Y.262, F.263, T.264, G.265, S.266, D.267, N.270 Chain B: A.6 Chain C: C.10 Ligands: MG.3, MG.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:D.267 Hydrogen bonds: A:R.140, A:S.171, A:R.174, A:R.174, A:G.180, A:D.181, A:D.183, A:N.270 Water bridges: A:S.171, A:S.171, A:D.181, A:D.267

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.181, D.183 Ligands: 4BD.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, A:D.183, H2O.1 MG.4: 6 residues within 4Å: Chain A: D.181, D.183, D.247 Chain C: C.10 Ligands: 4BD.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, A:D.183, A:D.247, H2O.1

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

NA.5: 4 residues within 4Å: Chain A: T.92, V.94, I.97 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.94, A:G.96, A:I.97 NA.6: 5 residues within 4Å: Chain A: K.51, L.53, P.54, V.56 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.51, A:V.56

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

CL.7: 3 residues within 4Å: Chain A: N.285, T.288, R.290 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: D.254, Q.255, Y.257, C.258, V.304 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Upton, T.G. et al., Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function. Org.Lett. (2009)

Release Date

2009-05-05

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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