SMTL ID : 6mq8.1

Binary structure of DNA polymerase eta in complex with templating hypoxanthine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 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: 31 residues within 4Å: Chain A: S.120, D.122, E.123, K.231, I.262, R.263, S.264, L.265, G.266, G.267, K.268, L.269, Q.372, R.384, L.385, L.388, R.389, R.390, C.391 Chain B: I.4, A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: 0KX.2, MG.4, NA.6 35 PLIP interactions: 35 interactions with chain A Hydrogen bonds: A:Y.46, A:W.71, A:K.324, A:T.325, A:T.325, A:G.327, A:S.329, A:N.331 Water bridges: A:Q.45, A:R.100, A:R.118, A:R.118, A:R.118, A:R.118, A:K.300, A:K.300, A:R.320, A:K.324, A:K.324, A:T.325, A:K.330, A:R.358, A:R.358, A:R.378 Salt bridges: A:K.93, A:R.100, A:R.100, A:K.300, A:K.300, A:K.318, A:R.320, A:K.324, A:K.330, A:R.358, A:R.358

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

0KX.2: 19 residues within 4Å: Chain A: D.20, M.21, D.22, C.23, F.24, F.25, I.55, A.56, Y.59, R.62, R.68, I.121, D.122, K.238 Chain B: I.4, A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, MG.3, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.25 Hydrogen bonds: A:D.22, A:C.23, A:F.24, A:F.25, A:Y.59, A:R.62, A:R.68, A:R.68 Water bridges: A:D.20, A:Y.59, A:R.62, A:R.62, A:R.68, A:S.120 Salt bridges: A:R.62, A:K.238

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: D.20, M.21, F.24, D.122, K.238 Ligands: 0KX.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.20, A:M.21, A:D.122 MG.4: 7 residues within 4Å: Chain A: D.20, S.120, D.122, E.123 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, 0KX.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.20, A:D.122, A:E.123, H2O.5

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

NA.5: 1 residues within 4Å: Chain A: D.365 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.365 NA.6: 2 residues within 4Å: Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, DA-DG-DC-DG-DT-DC-DA-DT.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jung, H. et al., Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase. Biochem.J. (2020)

Release Date

2019-10-23

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta