SMTL ID : 6m7p.1

Human DNA polymerase eta extension complex with cdA at the -2 position

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

DA-DG-DT-DG-DT-DG-DT-DG.1: 28 residues within 4Å: Chain A: 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.384, R.385, R.386, C.387 Chain B: T.4, C.5, X.6, C.7, A.8, C.9, A.10, C.11, T.12 Ligands: DZ4.2, MG.4 Protein-ligand interaction information (PLIP) not available

1 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.2: 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, I.117, D.118, K.234 Chain B: T.4, C.5 Ligands: DA-DG-DT-DG-DT-DG-DT-DG.1, MG.3, MG.4 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:M.17, A:C.19, A:F.20, A:F.21, A:Y.55, A:R.64 Water bridges: A:D.16, A:Q.41, A:Y.55, A:Y.55, A:R.58, A:R.58, A:R.58, A:R.58, A:R.58, A:R.64, A:S.116, A:K.227 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: DZ4.2, 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-DT-DG-DT-DG-DT-DG.1, DZ4.2, 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.7

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.250 Water bridges: A:T.282, A:T.282

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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