SMTL ID : 4dlg.1

Ternary Structure of the large Fragment of Taq DNA polymerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.1: 17 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, F.375, D.493 Chain B: C.12 Chain C: G.4, G.5 Ligands: MG.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.322, A:E.323, A:F.375, A:F.375, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:I.322, A:T.372, A:D.493 Water bridges: A:K.371, A:K.371, A:T.372 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

ACT.4: 5 residues within 4Å: Chain A: F.17, V.18, L.19, L.60, R.113 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.17, A:L.60 Hydrogen bonds: A:L.19 Water bridges: A:R.113, A:R.113 Salt bridges: A:R.113 ACT.5: 4 residues within 4Å: Chain A: D.79, W.125, R.139, R.143 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.125 Salt bridges: A:R.139, A:R.143 ACT.6: 3 residues within 4Å: Chain A: A.162, Y.163, A.166 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.166

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: N.193, S.194, R.195, D.196 Chain B: C.6 Chain C: G.11, T.12, G.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.194, A:R.195, A:D.196 Water bridges: A:N.193, A:N.193 GOL.8: 5 residues within 4Å: Chain B: A.2, C.3 Chain C: G.13, G.14, T.15 No protein-ligand interaction detected (PLIP) GOL.9: 4 residues within 4Å: Chain A: D.286, P.287 Chain C: C.9, C.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.286, A:D.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holzberger, B. et al., Structural insights into the potential of 4-fluoroproline to modulate biophysical properties of protein. Chem Sci (2012)

Release Date

2012-11-28

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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