SMTL ID : 5kfp.1

Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 20 mM Mg2+ for 600s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

DA-DG-DC-DG-DT-DC-DA-DT-AS.1: 42 residues within 4Å: Chain A: D.16, C.19, 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, K.379, L.381, L.384, R.385, R.386, C.387 Chain B: T.3, T.4, A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: MG.2, CA.3, MG.4, MG.5, STP.9, DPO.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.21, A:A.52 Hydrogen bonds: A:F.20, A:F.21 Water bridges: A:S.116

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 10 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-DT-AS.1, DA-DG-DC-DG-DT-DC-DA-DT-AS.1, CA.3, MG.4, MG.5, STP.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.4 MG.4: 9 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: DA-DG-DC-DG-DT-DC-DA-DT-AS.1, MG.2, CA.3, MG.5, STP.9, DPO.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MG.5: 7 residues within 4Å: Chain A: D.16 Ligands: DA-DG-DC-DG-DT-DC-DA-DT-AS.1, MG.2, CA.3, MG.4, STP.9, DPO.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.16, A:D.16, H2O.4, H2O.8

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 9 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: DA-DG-DC-DG-DT-DC-DA-DT-AS.1, MG.2, MG.4, MG.5, STP.9, DPO.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.282, A:T.282 GOL.7: 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:R.27, A:E.97, A:E.101 GOL.8: 3 residues within 4Å: Chain A: N.29, P.30, H.31 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.31

1 x STP: 2'-DEOXYADENOSINE 5'-O-(1-THIOTRIPHOSPHATE)(Non-covalent)

STP.9: 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.3, T.4, A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DT-AS.1, DA-DG-DC-DG-DT-DC-DA-DT-AS.1, MG.2, CA.3, MG.4, MG.5, DPO.10 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.21, A:A.52 Hydrogen bonds: A:D.18, A:C.19, A:F.20, A:F.21, A:Y.55 Water bridges: A:D.16, A:R.58, A:R.58, A:R.58, A:R.58, A:R.58, A:R.64, A:S.116 Salt bridges: A:R.58, A:R.58, A:R.64, A:K.234

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.10: 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-DT-AS.1, CA.3, MG.4, MG.5, STP.9 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:M.17, 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

Gao, Y. et al., Capture of a third Mg2+ is essential for catalyzing DNA synthesis. Science (2016)

Release Date

2016-06-22

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

Related Entries With Identical Sequence