SMTL ID : 5ytc.1

Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the unnatural base M-fC pair with dATP in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 16 residues within 4Å: Chain A: R.280, D.317, Y.318, S.319, Q.320, I.321, E.322, H.346, R.366, K.370, F.374, D.492 Chain B: C.13 Chain C: X.4, G.5 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.322, A:F.374 Hydrogen bonds: A:R.280, A:D.317, A:Q.320, A:I.321, A:E.322 Water bridges: A:K.370, A:K.370 Salt bridges: A:H.346, A:H.346, A:R.366, A:K.370, A:K.370, A:K.370

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

MG.2: 5 residues within 4Å: Chain A: D.317, D.492, E.493 Chain B: C.13 Ligands: DTP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.317, A:D.492, H2O.1 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, H. et al., Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew. Chem. Int. Ed. Engl. (2019)

Release Date

2018-11-21

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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