SMTL ID : 7m80.1

Human DNA Pol eta with dA-ended primer and dATP: in crystallo reaction for 100 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

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

DA-DG-DC-DG-DT-DC-DA-DA-DA.1: 40 residues within 4Å: Chain A: D.16, F.20, F.21, I.51, A.52, R.64, S.116, I.117, 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.2, T.3, T.4, T.5, G.6, A.7, C.8, G.9, C.10, T.11 Ligands: MG.2, CA.3, MG.4, DTP.8, DPO.9, MG.10 40 PLIP interactions: 40 interactions with chain A Hydrogen bonds: A:Q.41, A:I.50, A:S.65, A:W.67, A:K.320, A:T.321, A:G.323, A:S.325, A:N.327, A:N.327, A:R.354 Water bridges: A:A.90, A:A.90, A:R.96, A:R.96, A:R.96, A:R.114, A:R.114, A:N.297, A:R.316, A:R.316, A:R.316, A:K.320, A:T.321, A:R.354, A:R.354, A:R.374 Salt bridges: A:K.89, A:R.96, A:R.96, A:K.296, A:K.296, A:R.316, A:K.320, A:K.326, A:R.354 pi-Stacking: A:W.45, A:W.45, A:W.45, A:W.45

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: D.16, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-DA-DA.1, DA-DG-DC-DG-DT-DC-DA-DA-DA.1, CA.3, MG.4, DTP.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.8 MG.4: 8 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: DA-DG-DC-DG-DT-DC-DA-DA-DA.1, MG.2, CA.3, DTP.8, DPO.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.16, A:D.16, A:M.17, A:D.118 MG.10: 4 residues within 4Å: Chain A: R.64 Ligands: DA-DG-DC-DG-DT-DC-DA-DA-DA.1, DTP.8, DPO.9 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: DA-DG-DC-DG-DT-DC-DA-DA-DA.1, MG.2, MG.4, DTP.8, DPO.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.16, A:D.16, A:M.17, A:D.118

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.250 Water bridges: A:E.280, A:T.282, A:T.282 GOL.6: 3 residues within 4Å: Chain A: E.97, A.98, E.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.101 Water bridges: A:E.97, A:A.98, A:E.101 GOL.7: 3 residues within 4Å: Chain A: N.29, P.30, H.31 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.28, A:H.31

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.8: 24 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.2, T.3, T.4 Ligands: DA-DG-DC-DG-DT-DC-DA-DA-DA.1, DA-DG-DC-DG-DT-DC-DA-DA-DA.1, MG.2, CA.3, MG.4, DPO.9, MG.10 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:D.18, A:D.18, A:C.19, A:F.20, A:F.21, A:Y.55 Water bridges: A:Q.41, A:R.58, A:R.58, A:R.58, A:R.58, A:R.64 Salt bridges: A:R.58, A:R.58, A:R.64, A:R.64, A:K.234

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.9: 15 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, Y.55, R.58, R.64, D.118, K.234 Ligands: DA-DG-DC-DG-DT-DC-DA-DA-DA.1, CA.3, MG.4, DTP.8, MG.10 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:M.17, A:D.18, A:C.19, A:F.20, A:Y.55 Water bridges: A:D.16, A:R.58, A:R.58, A:R.58, A:R.58, A:R.64 Salt bridges: A:R.58, A:R.58, A:R.64, A:K.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gregory, M.T. et al., Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-06-02

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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