SMTL ID : 4nlk.1

Structure of human DNA polymerase beta complexed with 8BrG in the template base-paired with incoming non-hydrolyzable CTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 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: 19 residues within 4Å: Chain A: C.1, C.2, G.3, A.4, C.5 Chain C: 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 Ligands: NA.5 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.28, C:R.277 pi-Stacking: C:H.28

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

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

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

0KX.6: 18 residues within 4Å: Chain A: G.6 Chain B: A.10 Chain C: 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 Ligands: MG.2, MG.3 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:D.270 Hydrogen bonds: C:S.174, C:S.174, C:S.174, C:R.177, C:R.177, C:G.183, C:D.184, C:N.273 Water bridges: C:S.182, C:D.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.C. et al., Structural basis for promutagenicity of 8-halogenated Guanine. J.Biol.Chem. (2014)

Release Date

2014-01-22

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase beta

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