SMTL ID : 5kfo.1

Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 1 mM Mn2+ for 1800s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

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

DA-DG-DC-DG-DT-DC-DA-DT.1: 27 residues within 4Å: Chain A: S.116, 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: A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: MN.2, STP.7 Protein-ligand interaction information (PLIP) not available

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 8 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, CA.3, MN.4, STP.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.6 MN.4: 7 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: MN.2, CA.3, STP.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: MN.2, MN.4, STP.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118

2 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:T.282, A:T.282 GOL.6: 3 residues within 4Å: Chain A: N.29, P.30, H.31 No protein-ligand interaction detected (PLIP)

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

STP.7: 20 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, A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, MN.2, CA.3, MN.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:C.19, A:F.20, A:F.21, A:Y.55, A:Y.55, A:R.64 Water bridges: A:D.16, A:Y.55, A:R.58, A:R.58, A:R.58, A:R.64, A:R.64, A:R.64, A:S.116 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

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