SMTL ID : 3m8s.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x HXB: 4'-methylthymidine 5'-(tetrahydrogen triphosphate)(Non-covalent)

HXB.1: 18 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, D.493 Chain B: C.12 Chain C: A.4, G.5 Ligands: MG.2, MG.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.322, A:F.375, 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, 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: HXB.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.2, H2O.4 MG.3: 5 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: HXB.1, MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.380, E.450, E.453, R.454 Chain C: A.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.380, A:E.453, A:E.453, A:R.454 GOL.10: 4 residues within 4Å: Chain B: G.7, G.8, C.9 Chain C: C.9 No protein-ligand interaction detected (PLIP) GOL.11: 3 residues within 4Å: Chain C: G.5, G.6, C.7 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 5 residues within 4Å: Chain A: R.133, W.136, L.431, F.432, Y.519 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.133, A:L.431, A:F.432

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

15P.6: 8 residues within 4Å: Chain A: T.252, P.256, L.260, P.287, N.288, N.291 Chain C: C.9, C.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.288, A:N.291, A:N.291 Water bridges: A:N.288

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

ACT.7: 3 residues within 4Å: Chain A: R.21, W.26, L.260 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.26, A:L.260 Salt bridges: A:R.21 ACT.8: 5 residues within 4Å: Chain A: D.160, Y.163, R.304, I.307, D.534 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.163 Hydrogen bonds: A:D.534 ACT.9: 4 residues within 4Å: Chain A: R.436, Y.437, V.438 Ligands: ACT.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.438 Hydrogen bonds: A:Y.437 Water bridges: A:Y.437 Salt bridges: A:R.436 ACT.12: 4 residues within 4Å: Chain A: R.436 Chain C: G.6, C.7 Ligands: ACT.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.436

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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