SMTL ID : 7u7b.1

Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mM Mg2+ for 250s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

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

DA-DG-DC-DG-DT-DC-DA-DT-DG.1: 40 residues within 4Å: Chain A: D.16, F.20, F.21, Q.41, 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.3, T.4, A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: MG.2, DPO.5, DGT.6, MG.7, MG.8 Protein-ligand interaction information (PLIP) not available

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: DA-DG-DC-DG-DT-DC-DA-DT-DG.1, DPO.5, DGT.6, MG.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MG.7: 8 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-DT-DG.1, DA-DG-DC-DG-DT-DC-DA-DT-DG.1, MG.2, DGT.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.1, H2O.11 MG.8: 4 residues within 4Å: Chain A: R.64 Ligands: DA-DG-DC-DG-DT-DC-DA-DT-DG.1, DPO.5, DGT.6 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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:E.280, A:T.282 GOL.4: 4 residues within 4Å: Chain A: Q.28, N.29, P.30, H.31 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.28, A:H.31

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.5: 15 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, A.52, Y.55, R.58, R.64, D.118, K.234 Ligands: DA-DG-DC-DG-DT-DC-DA-DT-DG.1, MG.2, DGT.6, MG.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:M.17, A:C.19, A:F.20, A:Y.55 Water bridges: A:R.58, A:R.58, A:R.58, A:R.58 Salt bridges: A:R.58, A:R.58, A:R.64, A:K.234

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.6: 24 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, Q.41, 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-DG.1, DA-DG-DC-DG-DT-DC-DA-DT-DG.1, MG.2, DPO.5, MG.7, MG.8 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.21, A:A.52 Hydrogen bonds: A:D.16, A:C.19, A:F.20, A:F.21, A:Q.41, A:Q.41, A:Y.55, A:Y.55, A:R.64 Water bridges: A:R.58, A:R.58, A:R.58, A:R.58 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

Chang, C. et al., In crystallo observation of three metal ion promoted DNA polymerase misincorporation. Nat Commun (2022)

Release Date

2022-05-04

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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