SMTL ID : 4dfk.1

large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentinyl)-2-dUTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x 0L5: 2'-deoxy-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}uridine 5'-(tetrahydrogen triphosphate)(Non-covalent)

0L5.1: 24 residues within 4Å: Chain A: 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, D.493 Chain B: C.12 Chain C: A.4, G.5 Ligands: MG.2, MG.3, EDO.6 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:E.323, A:F.355, A:L.365, 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:T.372, A:T.372 Water bridges: A:R.367, A:R.367, A:K.371, A:K.371, A:Y.379, A:K.539, 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

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 5 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: 0L5.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MG.3: 5 residues within 4Å: Chain A: D.318, D.493 Chain B: C.12 Ligands: 0L5.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.7, H2O.7 MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: FMT.15 No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain C: G.5 No protein-ligand interaction detected (PLIP)

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: R.21, W.26, L.260 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.21, A:R.21 Water bridges: A:E.23, A:E.23 EDO.6: 7 residues within 4Å: Chain A: R.281, E.323, Q.462, A.465, A.466, H.492 Ligands: 0L5.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.281 EDO.11: 4 residues within 4Å: Chain A: D.160, R.304, I.307, D.534 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.160, A:D.534

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 5 residues within 4Å: Chain A: Y.253, P.287, N.288, N.291 Chain C: C.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.288, A:N.291, A:N.291 Water bridges: A:N.288 FMT.8: 3 residues within 4Å: Chain A: I.175, N.193, Y.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.193, A:Y.243 FMT.10: 1 residues within 4Å: Chain A: R.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.301 Water bridges: A:Y.163 FMT.12: 3 residues within 4Å: Chain A: L.60, K.62, D.63 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.62, A:K.62, A:D.63 Water bridges: A:A.61, A:K.62, A:K.62, A:K.62, A:R.271 FMT.15: 6 residues within 4Å: Chain A: N.193, S.194, R.195 Chain C: G.11, T.12 Ligands: MG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.195 Water bridges: A:D.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bergen, K. et al., Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates. J.Am.Chem.Soc. (2012)

Release Date

2012-05-16

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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