SMTL ID : 5e41.1

Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentenyl)-2'-deoxyuridine-triphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: D.318, D.493, E.494, K.539 Chain B: C.12 Ligands: MG.2, AUL.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.3, H2O.5 MG.2: 8 residues within 4Å: Chain A: D.318, Y.319, S.320, Q.321, I.322, D.493 Ligands: MG.1, AUL.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493

1 x AUL: 2'-deoxy-5-{(1E)-5-[(10-hydroxydecanoyl)amino]pent-1-en-1-yl}uridine 5'-(tetrahydrogen triphosphate)(Non-covalent)

AUL.3: 25 residues within 4Å: Chain A: E.228, R.281, R.295, D.318, Y.319, S.320, Q.321, I.322, E.323, H.347, F.355, L.365, R.367, R.368, A.369, K.371, T.372, F.375, Y.379, D.493 Chain B: C.12 Chain C: A.4, G.5 Ligands: MG.1, MG.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:E.323, A:L.365, A:R.368, A:A.369, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:I.322, A:E.323, A:R.368, A:R.368, A:T.372, A:T.372 Water bridges: A:R.281, A:R.367, A:R.367, A:K.371, A:K.371, A:Y.379, A:K.539 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 12 residues within 4Å: Chain A: T.252, Y.253, P.256, L.257, L.260, P.287, N.288, L.289, N.291, I.292 Chain C: C.9, C.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.288, A:N.291 Water bridges: A:D.286 GOL.5: 2 residues within 4Å: Chain A: K.501, E.533 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.533 GOL.6: 1 residues within 4Å: Chain A: K.475 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.475 GOL.7: 5 residues within 4Å: Chain A: A.278, R.436, M.455 Chain C: G.6, C.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hottin, A. et al., Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides. Chemistry (2017)

Release Date

2016-12-07

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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