SMTL ID : 6uqi.1

Crystal structure of Q38A human DNA polymerase eta bound with 8-oxoadenine (oxoA) and non-hydrolyzable dGTP analog (dGTP*)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x DA- DG- DC- DG- DT- DC- DA- DT: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')(Non-covalent)

DA-DG-DC-DG-DT-DC-DA-DT.1: 30 residues within 4Å: Chain A: R.64, S.116, D.118, E.119, K.227, I.258, R.259, S.260, L.261, G.262, G.263, K.264, L.265, R.380, L.381, L.384, R.385, R.386, C.387 Chain B: A.4, A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: XG4.2, MN.3 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: 19 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, I.51, A.52, Y.55, R.58, R.64, D.118, K.234 Chain B: T.3, A.4, A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, MN.3, MN.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:D.18, A:C.19, A:F.20, A:F.21, A:R.64 Water bridges: A:D.16, A:R.58, A:R.58, A:R.58, A:R.58 Salt bridges: A:R.58, A:K.234

2 x MN: MANGANESE (II) ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jung, H. et al., Crystal structure of Q38A human DNA polymerase eta bound with 8-oxoadenine (oxoA) and non-hydrolyzable dGTP analog (dGTP*). To Be Published

Release Date

2020-10-28

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta