SMTL ID : 5n2g.1

Structure of the E9 DNA polymerase from vaccinia virus in complex with manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

monomer

Ligands

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 7 residues within 4Å: Chain A: K.25, R.27, T.33, Y.194, T.259, F.260, D.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.259 Salt bridges: A:K.25, A:R.27 MES.2: 4 residues within 4Å: Chain A: R.306, Y.500, R.501, T.504 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.501, A:T.504, A:T.504 Salt bridges: A:R.306 MES.3: 10 residues within 4Å: Chain A: Y.304, H.323, V.324, F.332, F.333, D.334, S.337, S.495, F.498, E.499 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.334, A:S.337, A:F.498 Water bridges: A:F.332 Salt bridges: A:H.269, A:H.323, A:E.499

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

MN.4: 6 residues within 4Å: Chain A: D.170, I.171, E.172, Y.462, D.466 Ligands: MN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.170, A:E.172, A:D.466, H2O.2 MN.5: 3 residues within 4Å: Chain A: D.170, D.272 Ligands: MN.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.170, H2O.8 MN.6: 4 residues within 4Å: Chain A: D.553, N.555, E.794, E.796 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.794, A:E.796 MN.7: 1 residues within 4Å: Chain A: E.927 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.927

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: R.159, D.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.161 GOL.9: 8 residues within 4Å: Chain A: Y.118, I.119, G.122, I.123, P.125, S.488, V.491, K.512 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.122, A:S.488, A:K.512

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.10: 6 residues within 4Å: Chain A: E.343, Y.476, Y.477, K.482, D.658, Y.662 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.482

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 5 residues within 4Å: Chain A: H.174, E.210, M.211, L.212, T.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tarbouriech, N. et al., The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. Nat Commun (2017)

Release Date

2017-11-29

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase