SMTL ID : 7mz4.1

Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) in the template base paired with incoming dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 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.28, K.29, A.32, Y.33, L.56, P.57, G.58, V.59, G.60, T.61, K.62, I.63, K.66 Chain B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.5 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.28

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.184, D.186 Chain C: A.10 Ligands: MG.3, 1FZ.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.184, A:D.186, H2O.3 MG.3: 4 residues within 4Å: Chain A: D.184, D.186 Ligands: MG.2, 1FZ.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.184, H2O.1, H2O.2

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

NA.4: 6 residues within 4Å: Chain A: T.95, V.97, S.98, G.99, I.100 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.97, A:G.99, A:I.100 NA.5: 4 residues within 4Å: Chain A: K.54, L.56, V.59 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.59, A:V.59

1 x 1FZ: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine(Non-covalent)

1FZ.6: 19 residues within 4Å: Chain A: R.143, G.173, S.174, R.177, S.182, G.183, D.184, D.186, Y.265, F.266, T.267, G.268, S.269, D.270, N.273 Chain B: A.6 Chain C: A.10 Ligands: MG.2, MG.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.143, A:S.174, A:S.174, A:R.177, A:R.177, A:G.183, A:D.184, A:D.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.-C. et al., Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) in the template base paired with incoming dTTP. To Be Published

Release Date

2022-06-01

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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