SMTL ID : 6m7o.1

Human DNA polymerase eta ternary complex with Mn2+ and dTMPNPP oppositing cdA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x DA- DG- DT- DG- DT- DG- DA- DG: DNA (5'-D(P*AP*GP*TP*GP*TP*GP*AP*G*(1FZ))-3')(Non-covalent)

DA-DG-DT-DG-DT-DG-DA-DG.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, K.431 Chain B: C.4, T.5, C.6, A.7, C.8, A.9, C.10, T.11 Ligands: MN.3, 1FZ.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.96, A:K.320, A:T.321, A:T.321, A:G.323, A:S.325, A:N.327, A:N.327 Salt bridges: A:K.89, A:R.96, A:R.316, A:R.316, A:K.320, A:K.326, A:R.354

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

MN.2: 5 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: MN.3, 1FZ.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MN.3: 7 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DT-DG-DT-DG-DA-DG.1, MN.2, 1FZ.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:D.118, A:E.119

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

1FZ.4: 17 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: X.3 Ligands: DA-DG-DT-DG-DT-DG-DA-DG.1, MN.2, MN.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:M.17, A:C.19, A:F.20, A:F.21, A:Y.55 Water bridges: A:S.116 Salt bridges: A:R.58, A:K.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weng, P.J. et al., Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-09-12

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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