SMTL ID : 7m7m.1

Human DNA Pol eta with rA-ended primer and dAMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

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

DA-DG-DC-DG-DT-DC-DA-A.1: 29 residues within 4Å: Chain A: 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.4, T.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: DZ4.2, MG.4 Protein-ligand interaction information (PLIP) not available

2 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, T.5 Ligands: DA-DG-DC-DG-DT-DC-DA-A.1, MG.3, MG.4 18 PLIP interactions: 18 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.58 Water bridges: A:D.16, A:D.16, A:Y.55, A:R.58, A:R.58, A:R.64, A:R.64, A:R.64, A:R.64 Salt bridges: A:R.58, A:K.234 DZ4.5: 5 residues within 4Å: Chain A: S.260, L.265, K.296, N.297, W.300 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.260, A:K.296, A:N.297 pi-Stacking: A:W.300, A:W.300, A:W.300 pi-Cation interactions: A:K.296

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-DC-DG-DT-DC-DA-A.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

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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.247 Water bridges: A:T.282, A:T.282 GOL.7: 6 residues within 4Å: Chain A: Q.23, Q.26, R.27, R.33, G.212, F.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.23, A:R.27 Water bridges: A:Q.26, A:Q.26, A:R.33 GOL.8: 5 residues within 4Å: Chain A: G.274, I.275, E.276, Y.277, E.280 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.274, A:E.276 Water bridges: A:E.276, A:E.280, A:E.280

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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