SMTL ID : 4tur.1

Human DNA polymerase beta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

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

DG-DT-DG-DG-DG.1: 19 residues within 4Å: Chain A: H.28, K.29, A.32, Y.33, L.56, P.57, G.58, V.59, G.60, T.61, K.62, I.63, K.66 Chain B: C.1, C.2, C.3, A.4, C.5 Ligands: NA.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.31 Salt bridges: A:R.277 pi-Stacking: A:H.28

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.184, D.186 Ligands: MG.3, 0KX.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.184, H2O.4, H2O.4 MG.3: 6 residues within 4Å: Chain A: D.184, D.186, D.250 Chain C: C.10 Ligands: MG.2, 0KX.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.184, A:D.186

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

NA.4: 6 residues within 4Å: Chain A: T.95, V.97, S.98, G.99, I.100 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.99, A:I.100, A:I.100 NA.5: 4 residues within 4Å: Chain A: K.54, L.56, V.59 Ligands: DG-DT-DG-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.59, A:V.59

1 x 0KX: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine(Non-covalent)

0KX.6: 20 residues within 4Å: Chain A: R.143, G.173, S.174, R.177, S.182, G.183, D.184, D.186, Y.265, F.266, T.267, G.268, S.269, D.270, N.273 Chain B: G.6, G.7 Chain C: C.10 Ligands: MG.2, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.143, A:S.174, A:S.174, A:R.177, A:R.177, A:G.183, A:D.184, A:S.269, A:N.273 Water bridges: A:D.184, A:D.184

1 x CPT: Cisplatin(Non-covalent)

CPT.7: 3 residues within 4Å: Chain A: N.31 Chain B: G.6, G.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.C. et al., Structural Basis for the Inefficient Nucleotide Incorporation Opposite Cisplatin-DNA Lesion by Human DNA Polymerase beta. J.Biol.Chem. (2014)

Release Date

2014-10-01

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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