SMTL ID : 5szt.1

Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

MG.1: 7 residues within 4Å: Chain A: D.318, Y.319, Q.321, I.322, D.493 Ligands: MG.2, 72J.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MG.2: 7 residues within 4Å: Chain A: D.318, D.493, E.494, K.539 Chain B: C.12 Ligands: MG.1, 72J.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.3, H2O.4 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.288, A:N.291 Water bridges: A:Y.253, A:D.286 GOL.9: 5 residues within 4Å: Chain C: T.4, G.5, G.6, C.7 Ligands: ACT.10 No protein-ligand interaction detected (PLIP)

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

ACT.4: 4 residues within 4Å: Chain A: R.21, W.26, D.259, L.260 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.26 Water bridges: A:R.21 Salt bridges: A:R.21 ACT.5: 4 residues within 4Å: Chain A: R.133, W.136, F.432, Y.519 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.133 ACT.6: 6 residues within 4Å: Chain A: R.57, D.79, F.121, W.125, R.139, R.143 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.125 Hydrogen bonds: A:R.139 Salt bridges: A:R.143 ACT.10: 5 residues within 4Å: Chain A: A.278, R.436 Chain C: G.6, C.7 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.436

1 x 72J: 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP(Non-covalent)

72J.7: 27 residues within 4Å: Chain A: R.281, R.295, D.318, Y.319, S.320, Q.321, I.322, E.323, L.324, H.347, M.354, F.355, R.367, R.368, A.369, K.371, T.372, F.375, Y.379, E.389, H.492, D.493 Chain B: C.12 Chain C: T.4, G.5 Ligands: MG.1, MG.2 24 PLIP interactions: 24 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, A:T.372 Water bridges: A:R.281, A:D.318, A:Y.319, A:R.367, A:R.367, A:K.371, A:T.372, 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

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

2016-12-14

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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