SMTL ID : 4mfa.1

Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template O6MG and incoming TTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 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: 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 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.24

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

NA.2: 5 residues within 4Å: Chain A: T.91, V.93, S.94, I.96 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.93, A:G.95, A:I.96 NA.4: 5 residues within 4Å: Chain A: K.50, K.51, L.52, V.55 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.50, A:G.54, A:V.55

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: S.161 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.161, H2O.1 MG.6: 5 residues within 4Å: Chain A: D.180, D.182, D.246 Chain C: A.10, T.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.180

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain A: R.139, G.169, S.170, S.178, G.179, D.180 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.139, A:S.170, A:S.170, A:S.178, A:G.179, A:D.180, A:D.180 Water bridges: A:R.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.C. et al., Structures of human DNA polymerase beta inserting bases opposite templating O6MG. To be Published

Release Date

2014-08-27

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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