SMTL ID : 4dfm.1

Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in ternary complex with 5-(aminopentinyl)-2-dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x 0L6: 5-(5-aminopent-1-yn-1-yl)-2'-deoxycytidine 5'-(tetrahydrogen triphosphate)(Non-covalent)

0L6.1: 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.11, G.12 Chain C: G.4, C.5 Ligands: MG.2, MG.3, EDO.6 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:E.323, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:I.322, A:E.323, A:T.372 Water bridges: A:D.318, 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

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

MG.2: 5 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: 0L6.1, 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: G.12 Ligands: 0L6.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.1, H2O.1 MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

FMT.4: 4 residues within 4Å: Chain A: E.45, P.46, Y.47, K.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.47, A:K.48

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

EDO.6: 7 residues within 4Å: Chain A: R.281, E.323, Q.462, A.465, A.466, H.492 Ligands: 0L6.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.281, A:E.323 EDO.7: 6 residues within 4Å: Chain A: L.60, K.62, D.63, F.272, N.273, 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.8: 6 residues within 4Å: Chain A: G.104, E.105, E.112, A.115, L.116, R.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.105, A:E.105, A:R.119, A:R.119 EDO.9: 7 residues within 4Å: Chain A: T.252, Y.253, L.257, P.287, N.288, N.291 Chain C: C.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.252, A:Y.253, A:N.291, A:N.291 EDO.10: 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

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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