SMTL ID : 4ny8.1

DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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: 17 residues within 4Å: Chain A: K.26, A.29, Y.30, L.53, P.54, G.55, V.56, G.57, T.58, K.59, I.60, K.63 Chain B: C.1, C.2, G.3, A.4, C.5 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.25

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

MN.2: 4 residues within 4Å: Chain A: D.181, D.183 Ligands: MN.3, 0KX.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, A:D.183, H2O.1 MN.3: 5 residues within 4Å: Chain A: D.181, D.183 Chain C: A.10 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.4

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

NA.4: 2 residues within 4Å: Chain A: T.92 Ligands: NA.5 No protein-ligand interaction detected (PLIP) NA.5: 7 residues within 4Å: Chain A: T.92, V.94, S.95, G.96, I.97 Chain C: G.9 Ligands: NA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.96, A:I.97, A:I.97

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: R.140, G.170, S.171, R.174, S.179, G.180, D.181, D.183, Y.262, F.263, G.265, S.266, D.267, N.270 Chain B: G.6 Ligands: MN.2, MN.3 11 PLIP interactions: 11 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:D.181, A:N.270 Water bridges: A:D.267, A:D.267 Salt bridges: A:R.140

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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