SMTL ID : 5yth.1

Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base M-fC pair with dG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

monomer

Ligands

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 19 residues within 4Å: Chain A: R.280, D.317, Y.318, S.319, Q.320, I.321, E.322, H.346, R.366, R.367, K.370, F.374, Y.378, D.492 Chain B: C.12 Chain C: C.4, G.5 Ligands: MG.2, MG.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:E.322, A:F.374 Hydrogen bonds: A:R.280, A:S.319, A:Q.320, A:I.321, A:E.322, A:R.367, A:R.367 Water bridges: A:K.370, A:N.457, A:K.538 Salt bridges: A:H.346, A:R.366, A:K.370, A:K.370, A:K.370 pi-Stacking: A:F.374, A:F.374

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.317, Y.318, D.492 Ligands: DGT.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.317, A:Y.318, A:D.492 MG.3: 6 residues within 4Å: Chain A: D.317, D.492, K.538 Chain B: C.12 Ligands: DGT.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.317, A:D.492, H2O.1, H2O.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: T.251, P.255, D.285, P.286, N.287 Chain C: C.9, C.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.251, A:N.287

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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