SMTL ID : 5omq.1

Ternary complex of 9N DNA polymerase in the replicative state with three metal ions in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: Y.402, H.545, Y.583, Y.594, R.606 Chain C: C.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.545, A:Y.583, A:Y.583, A:R.606

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 5 residues within 4Å: Chain A: N.210, Y.261, Y.273, G.696, T.697 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.696

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: Y.402, D.404, D.542, G.543 Chain C: C.12 Ligands: MN.5, DTP.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.404, A:D.542, H2O.2, H2O.3 MG.4: 5 residues within 4Å: Chain A: D.404, F.405, E.580 Ligands: MN.5, DTP.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.404, A:E.580, H2O.1, H2O.2, H2O.2

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

MN.5: 6 residues within 4Å: Chain A: D.404, F.405, D.542 Ligands: MG.3, MG.4, DTP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.404, A:F.405, A:D.542

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

DTP.6: 20 residues within 4Å: Chain A: D.404, F.405, R.406, S.407, L.408, Y.409, P.410, R.460, K.487, I.488, N.491, Y.494, T.541, D.542 Chain B: T.4, G.5 Chain C: C.12 Ligands: MG.3, MG.4, MN.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.409 Hydrogen bonds: A:S.407, A:L.408, A:Y.409, A:N.491, A:N.491 Water bridges: A:D.404, A:K.464, A:K.464, A:E.580 Salt bridges: A:R.460, A:K.464, A:K.487, A:K.487, A:K.487

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kropp, H.M. et al., Crystal structures of ternary complexes of archaeal B-family DNA polymerases. PLoS ONE (2017)

Release Date

2017-12-20

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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