SMTL ID : 5nkl.1

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dDs-dPxTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: D.318, D.493, E.494, K.539 Chain B: C.12 Ligands: MG.2, 91T.4, 91R.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.1, H2O.7 MG.2: 8 residues within 4Å: Chain A: D.318, Y.319, S.320, Q.321, D.493 Ligands: MG.1, 91T.4, 91R.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: R.133, W.136, F.432, Y.519 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.136 Salt bridges: A:R.133

1 x 91T: [[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

91T.4: 24 residues within 4Å: Chain A: R.281, R.295, D.318, Y.319, S.320, Q.321, I.322, E.323, H.347, R.367, R.368, K.371, T.372, F.375, Y.379, H.492, D.493 Chain B: C.11, C.12 Chain C: X.4, G.5 Ligands: MG.1, MG.2, 91R.5 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:E.323, A:K.371, A:F.375 Hydrogen bonds: A:R.281, A:S.320, A:Q.321, A:I.322, A:E.323, A:R.368, A:D.493 Water bridges: A:R.281, A:R.367, A:R.367, A:K.371, A:K.371 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375

1 x 91R: [[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

91R.5: 26 residues within 4Å: Chain A: R.281, V.294, R.295, D.318, Y.319, S.320, Q.321, I.322, E.323, L.324, H.347, R.367, R.368, K.371, T.372, F.375, Y.379, H.492, D.493 Chain B: C.11, C.12 Chain C: X.4, G.5 Ligands: MG.1, MG.2, 91T.4 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:E.323, A:F.375 Hydrogen bonds: A:R.281, A:S.320, A:Q.321, A:I.322, A:E.323, A:R.368, A:D.493, A:D.493 Water bridges: A:R.281, A:D.318, A:R.367, A:R.367, A:K.371 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: R.385 Chain B: G.10, C.11, C.12 Chain C: X.4, G.5, G.6 Ligands: GOL.7 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain C: X.4, G.5, G.6, C.7 Ligands: GOL.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Betz, K. et al., Structural Basis for Expansion of the Genetic Alphabet with an Artificial Nucleobase Pair. Angew. Chem. Int. Ed. Engl. (2017)

Release Date

2017-06-28

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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