SMTL ID : 5kfs.1

Human DNA polymerase eta R61A-DNA ternary complex: ground state at pH7.0 (K+ MES) with 1 Ca2+ ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 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: DTP.6, K.7 Protein-ligand interaction information (PLIP) not available

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: DTP.6, K.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118

3 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:T.282, A:T.282 GOL.4: 3 residues within 4Å: Chain A: E.97, A.98, E.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.101 Water bridges: A:E.97 GOL.5: 3 residues within 4Å: Chain A: N.29, P.30, H.31 No protein-ligand interaction detected (PLIP)

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

DTP.6: 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, I.117, D.118, K.234 Chain B: T.3, T.4, A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, CA.2, K.7 16 PLIP interactions: 16 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 Water bridges: A:Q.41, A:R.58, A:R.58, A:R.58, A:R.58, A:E.119, A:E.119 Salt bridges: A:R.58, A:R.58, A:K.234

1 x K: POTASSIUM ION(Non-covalent)

K.7: 7 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, CA.2, DTP.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.118, A:E.119

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

2016-06-29

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

Related Entries With Identical Sequence