SMTL ID : 7mz2.1

Structure of human DNA polymerase beta complexed with dzA at N-1 of the template base paired with incoming dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 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: 18 residues within 4Å: Chain A: H.25, K.26, A.29, Y.30, L.53, P.54, G.55, V.56, G.57, T.58, K.59, I.60 Chain B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.270, A:R.274, A:R.274 Water bridges: A:N.28, A:N.28 Salt bridges: A:K.271 pi-Stacking: A:H.25

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.181, D.183 Ligands: MG.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 MG.3: 6 residues within 4Å: Chain A: D.181, D.183, D.247 Chain C: T.10 Ligands: MG.2, 0KX.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, A:D.183, A:D.247, H2O.1

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

NA.4: 6 residues within 4Å: Chain A: T.92, V.94, S.95, G.96, I.97 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.96, A:I.97, A:I.97 NA.5: 4 residues within 4Å: Chain A: K.51, L.53, V.56 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.51, A:V.56

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

0KX.6: 18 residues within 4Å: Chain A: G.170, S.171, R.174, S.179, G.180, D.181, D.183, Y.262, F.263, T.264, G.265, S.266, D.267, N.270 Chain B: G.6 Chain C: T.10 Ligands: MG.2, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.267 Hydrogen bonds: A:S.171, A:S.171, A:S.171, A:R.174, A:R.174, A:G.180, A:D.181, A:N.270 Water bridges: A:D.267, A:D.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.-C. et al., Structure of human DNA polymerase beta complexed with dzA at N-1 of the template base paired with incoming dTTP. To Be Published

Release Date

2022-05-25

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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