SMTL ID : 4m47.1

structure of human DNA polymerase complexed with 8-BrG in the template base paired with incoming non-hydrolyzable GTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: a synthetic downstream primer(Non-covalent)

DG-DT-DC-DG-DG.1: 19 residues within 4Å: Chain A: H.23, K.24, A.27, Y.28, L.51, P.52, G.53, V.54, G.55, T.56, K.57, I.58, K.61 Chain B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.6 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.23

1 x XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.2: 18 residues within 4Å: Chain A: G.168, S.169, R.172, S.177, G.178, D.179, D.181, Y.260, F.261, T.262, G.263, D.265, N.268 Chain B: G.6, T.7 Chain C: A.10 Ligands: MG.3, NA.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.169, A:S.169, A:S.169, A:R.172, A:R.172, A:G.178, A:D.179, A:Y.260 Water bridges: A:R.138, A:D.179, A:R.272 Salt bridges: A:D.265

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.179, D.181 Ligands: XG4.2, NA.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.179, A:D.181, H2O.2

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

NA.4: 4 residues within 4Å: Chain A: D.179, D.181 Ligands: XG4.2, MG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.179 NA.5: 6 residues within 4Å: Chain A: T.90, V.92, S.93, G.94, I.95 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.92, A:G.94, A:I.95 NA.6: 4 residues within 4Å: Chain A: K.49, L.51, V.54 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.54, A:V.54

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta