SMTL ID : 7m85.1

Human DNA Pol eta S113A with dA-ended primer and dATP: in crystallo reaction for 80 s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

DA-DG-DC-DG-DT-DC-DA-DA.1: 29 residues within 4Å: Chain A: A.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.4, T.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: DTP.5, MG.6 Protein-ligand interaction information (PLIP) not available

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: MG.3, DTP.5, MG.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.16, A:D.16, A:M.17, A:D.118

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: CA.2, DTP.5, MG.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.16, A:D.16, A:M.17, A:D.118 MG.6: 7 residues within 4Å: Chain A: D.16, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-DA.1, CA.2, MG.3, DTP.5 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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:P.247 Water bridges: A:E.280, A:T.282, A:T.282

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

DTP.5: 21 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, T.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DA.1, CA.2, MG.3, MG.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:D.16, A:C.19, A:F.20, A:F.21, A:Y.55, A:Y.55 Water bridges: A:Q.41, A:R.58, A:R.58, A:R.58, A:R.64, A:R.64, A:R.64, A:E.119, A:E.119 Salt bridges: A:R.58, A:R.58, A:R.64, 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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