SMTL ID : 4df8.1

Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with aminopentinyl-7-deaza-2-dATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 0L4: 5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine(Non-covalent)

0L4.1: 21 residues within 4Å: Chain A: R.281, D.318, Y.319, S.320, Q.321, I.322, E.323, H.347, R.367, R.368, K.371, T.372, F.375, D.493 Chain B: C.12 Chain C: T.4, G.5 Ligands: MG.2, MG.3, EDO.7, CL.10 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:E.323, A:R.368, A:T.372, A:F.375, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:I.322, A:E.323, A:R.368, A:K.371 Water bridges: A:D.318, A:R.367, A:K.371, A:K.539 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371

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

MG.2: 5 residues within 4Å: Chain A: D.318, D.493 Chain B: C.12 Ligands: 0L4.1, MG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.318, A:D.493, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: 0L4.1, MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.4: 5 residues within 4Å: Chain A: L.60, K.62, D.63, F.272, Q.274 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.62, A:D.63, A:D.63, A:F.272, A:Q.274 Water bridges: A:R.271, A:R.271, A:T.275 EDO.7: 7 residues within 4Å: Chain A: R.281, E.323, Q.462, A.465, A.466, H.492 Ligands: 0L4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.281, A:E.323 Water bridges: A:H.492 EDO.9: 7 residues within 4Å: Chain A: D.196, K.219 Chain B: C.6, G.7 Chain C: G.11, T.12, G.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.196 EDO.12: 3 residues within 4Å: Chain C: G.5, G.6 Ligands: FMT.13 No protein-ligand interaction detected (PLIP)

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

FMT.5: 4 residues within 4Å: Chain A: F.17, V.18, L.19, R.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.17, A:L.19, A:R.113 FMT.8: 3 residues within 4Å: Chain A: G.380, F.405, R.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.412 FMT.13: 4 residues within 4Å: Chain C: T.4, G.5, G.6 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) FMT.14: 3 residues within 4Å: Chain A: R.436 Chain C: G.6, C.7 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: R.21, W.26 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: R.368, K.371 Ligands: 0L4.1 Ligand excluded by PLIP

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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