SMTL ID : 4dle.1

Ternary Structure of the large Fragment of Taq DNA Polymerase: 4-Fluoroproline Variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.318, D.493, E.494 Chain B: C.12 Ligands: DCT.3, MN.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.1, H2O.5

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: T.252, Y.253, P.256, 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.288 Water bridges: A:D.286, A:N.288 GOL.6: 4 residues within 4Å: Chain B: C.6, G.7, G.8 Chain C: C.9 No protein-ligand interaction detected (PLIP)

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

DCT.3: 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: G.4, G.5 Ligands: MG.1, MN.4 15 PLIP interactions: 15 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:S.320, A:Q.321, A:I.322 Water bridges: A:K.371 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 5 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: MG.1, DCT.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493

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

EDO.5: 6 residues within 4Å: Chain A: R.158, A.308, E.309, G.311, W.312, E.533 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.158, A:W.312, A:W.312, A:E.533

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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