SMTL ID : 7m7s.1

Human DNA Pol eta S113A with dT-ended primer and 0.1 mM dAMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x DT- DA- DG- DC- DG- DT- DC- DA- DT: DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')(Non-covalent)

DT-DA-DG-DC-DG-DT-DC-DA-DT.1: 26 residues within 4Å: Chain A: R.64, K.227, I.258, R.259, S.260, L.261, G.262, G.263, K.264, L.265, Q.368, R.380, L.384, R.385, R.386, C.387 Chain B: T.4, A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: DZ4.2 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: 17 residues within 4Å: Chain A: M.17, D.18, C.19, F.20, F.21, I.51, A.52, Y.55, R.58, R.64, D.118, K.234 Chain B: T.4, A.5 Ligands: DT-DA-DG-DC-DG-DT-DC-DA-DT.1, MG.3, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:M.17, A:D.18, A:C.19, A:F.20, A:F.21, A:Y.55, A:R.58, A:R.64, A:D.118 Water bridges: A:Y.55, A:R.58, A:R.58, A:K.234 Salt bridges: A:R.58, A:K.234 DZ4.8: 4 residues within 4Å: Chain A: S.260, K.296, N.297, W.300 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.260, A:S.260 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: 5 residues within 4Å: Chain A: M.17, C.19, D.118 Ligands: DZ4.2, MG.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.17, H2O.7 MG.4: 5 residues within 4Å: Chain A: D.16, D.118, E.119 Ligands: DZ4.2, MG.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.118, H2O.1

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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.6: 5 residues within 4Å: Chain A: Q.23, Q.26, R.27, R.33, G.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.23 Water bridges: A:Q.26, A:Q.26 GOL.7: 3 residues within 4Å: Chain A: N.29, P.30, H.31 No protein-ligand interaction detected (PLIP) GOL.9: 6 residues within 4Å: Chain A: T.321, F.426, C.428 Chain B: G.7, A.8, C.9 5 PLIP interactions: 5 interactions with chain A Water bridges: A:T.321, A:T.321, A:T.321, A:R.385, A:R.385

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

Related Entries With Identical Sequence