SMTL ID : 3m8r.1

Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in a closed ternary complex with trapped 4'-ethylated dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x HXZ: 4'-ethylthymidine 5'-(tetrahydrogen triphosphate)(Non-covalent)

HXZ.1: 19 residues within 4Å: Chain A: R.281, D.318, Y.319, S.320, Q.321, I.322, E.323, H.347, R.367, K.371, T.372, F.375, H.492, D.493 Chain B: C.12 Chain C: A.4, G.5 Ligands: MG.2, MG.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.322, A:E.323, A:E.323, A:F.375, A:H.492, A:D.493 Hydrogen bonds: A:R.281, A:Q.321, A:I.322, A:E.323 Water bridges: 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.318, D.493 Chain B: C.12 Ligands: HXZ.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.1, H2O.7 MG.3: 5 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: HXZ.1, MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493

2 x 15P: POLYETHYLENE GLYCOL (N=34)(Non-functional Binders)

15P.4: 11 residues within 4Å: Chain A: E.23, W.26, L.260, L.268, H.269, D.286, P.287 Chain C: C.9, C.10 Ligands: GOL.5, ACT.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.260, A:H.269, A:D.286, A:D.286 Water bridges: A:K.22, A:E.23, A:D.286 15P.7: 3 residues within 4Å: Chain A: L.169, E.170, E.173 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: T.252, Y.253, P.256, L.257, P.287, N.288, N.291 Chain C: C.9, C.10 Ligands: 15P.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.288, A:N.288, A:N.291 GOL.6: 7 residues within 4Å: Chain A: N.193, S.194, R.195, D.196 Chain C: G.11, T.12, G.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.193, A:S.194, A:R.195, A:D.196 GOL.9: 4 residues within 4Å: Chain B: C.6, G.7, G.8 Chain C: C.9 No protein-ligand interaction detected (PLIP) GOL.10: 2 residues within 4Å: Chain C: G.5, G.6 No protein-ligand interaction detected (PLIP)

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

ACT.8: 4 residues within 4Å: Chain A: R.21, W.26, L.260 Ligands: 15P.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.26, A:L.260 Salt bridges: A:R.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Betz, K. et al., Structures of DNA polymerases caught processing size-augmented nucleotide probes. Angew.Chem.Int.Ed.Engl. (2010)

Release Date

2010-07-07

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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