SMTL ID : 6pkz.1

Structure of human DNA polymerase beta N279A complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: DNA (5'-D(P*GP*TP*CP*GP*G)-3')(Non-covalent)

DG-DT-DC-DG-DG.1: 19 residues within 4Å: Chain A: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69, K.72 Chain B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.3 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.34

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

NA.2: 5 residues within 4Å: Chain A: T.101, V.103, S.104, I.106 Chain C: G.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.101 NA.3: 4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.62

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.190, D.192 Ligands: XG4.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.190, A:D.192

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

XG4.5: 16 residues within 4Å: Chain A: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, S.275, D.276 Chain B: A.6 Chain C: A.10 Ligands: MG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:G.189, A:D.190 Salt bridges: A:D.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.C. et al., Structure of human DNA polymerase beta N279A complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP. To Be Published

Release Date

2020-07-01

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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