SMTL ID : 4tus.1

Human DNA polymerase beta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2) WITH MANGANESE IN THE ACTIVE SITE.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 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: 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, C.3, A.4, C.5 Ligands: NA.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.271 Salt bridges: A:K.271, A:R.274 pi-Stacking: A:H.25

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: D.181, D.183, D.247 Chain C: C.10 Ligands: MN.3, 0KX.6 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 MN.3: 4 residues within 4Å: Chain A: D.181, D.183 Ligands: MN.2, 0KX.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, A:D.183, H2O.1

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

NA.4: 6 residues within 4Å: Chain A: T.92, V.94, S.95, G.96, I.97 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.96, A:I.97, A:I.97 NA.5: 4 residues within 4Å: Chain A: K.51, L.53, V.56 Ligands: DG-DT-DG-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.51

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

0KX.6: 17 residues within 4Å: Chain A: G.170, S.171, R.174, S.179, G.180, D.181, D.183, Y.262, F.263, T.264, G.265, D.267, N.270 Chain B: G.6 Chain C: C.10 Ligands: MN.2, MN.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.171, A:S.171, A:R.174, A:R.174, A:G.180, A:D.181, A:Y.262, A:N.270 Water bridges: A:F.172, A:F.172

1 x CPT: Cisplatin(Non-covalent)

CPT.7: 4 residues within 4Å: Chain A: N.28, K.271 Chain B: G.6, G.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.28, A:K.271, A:K.271

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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