SMTL ID : 6pz3.1

Polymerase Eta-catalyzed insertion of correct G opposite template cytarabine (AraC) residue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

1 x DA- DG- DC- DA- DC- DT- DG- DT: DNA Primer strand(Non-covalent)

DA-DG-DC-DA-DC-DT-DG-DT.1: 30 residues within 4Å: Chain A: D.16, S.116, D.118, E.119, K.227, I.258, R.259, S.260, L.261, G.262, G.263, K.264, L.265, Q.368, R.380, L.384, R.385, R.386, C.387 Chain B: C.4, A.5, C.6, A.7, G.8, T.9, G.10, C.11, T.12 Ligands: XG4.2, MG.4 Protein-ligand interaction information (PLIP) not available

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

XG4.2: 25 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, V.22, Q.41, I.51, A.52, V.53, Y.55, R.58, R.64, S.116, I.117, D.118, E.119, K.234 Chain B: T.3, C.4, A.5 Ligands: DA-DG-DC-DA-DC-DT-DG-DT.1, MG.3, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:M.17, A:D.18, A:C.19, A:F.20, A:F.21, A:Q.41, A:Y.55, A:R.64, A:R.64, A:R.64 Water bridges: A:R.58, A:R.58, A:R.58, A:R.58 Salt bridges: A:R.58, A:K.234

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: XG4.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MG.4: 7 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DC-DA-DC-DT-DG-DT.1, XG4.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.1

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: P.247, Q.248, F.250, S.251, G.279, E.280, T.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rechkoblit, O. et al., Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase eta. Sci Rep (2019)

Release Date

2019-11-20

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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