SMTL ID : 4mfc.1

Structure of human DNA polymerase beta complexed with O6MG in the template base paired with incoming non-hydrolyzable CTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: dn primer(Non-covalent)

DG-DT-DC-DG-DG.1: 18 residues within 4Å: Chain A: H.24, K.25, A.28, Y.29, L.52, P.53, G.54, V.55, G.56, T.57, K.58, I.59, K.62 Chain B: C.1, C.2, G.3, A.4, C.5 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.24

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.180 Ligands: 0KX.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.180, H2O.4, H2O.4

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

NA.3: 2 residues within 4Å: Chain A: T.91 Ligands: NA.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.17, A:T.91, A:T.91 NA.4: 7 residues within 4Å: Chain A: T.91, V.93, S.94, G.95, I.96 Chain C: G.9 Ligands: NA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.93, A:G.95, A:I.96

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

0KX.5: 15 residues within 4Å: Chain A: R.139, G.169, S.170, R.173, S.178, G.179, D.180, Y.261, F.262, T.263, G.264, D.266, N.269 Chain B: G.6 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.170, A:S.170, A:R.173, A:R.173, A:G.179, A:D.180, A:Y.261, A:N.269 Water bridges: A:D.180 Salt bridges: A:R.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.C. et al., Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta. J.Am.Chem.Soc. (2014)

Release Date

2014-04-16

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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