SMTL ID : 5z3n.1

Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

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

MG.1: 5 residues within 4Å: Chain A: D.317, Y.318, D.492 Ligands: MG.2, DGT.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.317, A:Y.318, A:D.492 MG.2: 5 residues within 4Å: Chain A: D.317, D.492 Chain B: C.12 Ligands: MG.1, DGT.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.317, A:D.492, H2O.4, H2O.17 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

DGT.3: 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.1, MG.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:E.322, A:F.374 Hydrogen bonds: A:R.280, A:Q.320, A:I.321, A:E.322, A:R.367, A:R.367 Water bridges: A:Y.318, A:S.319, A:E.322, A:K.370, A:N.457, A:K.538, 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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: E.169, V.170, E.173, L.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.169, A:E.169, A:E.173 GOL.5: 8 residues within 4Å: Chain A: T.251, Y.252, P.255, P.286, N.287, N.290 Chain C: C.9, C.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.287, A:N.290 Water bridges: A:Y.252, A:D.285 GOL.6: 1 residues within 4Å: Chain A: E.532 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain A: R.132, W.135, L.430, F.431, Y.518 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.430, A:Y.518, A:Y.518 GOL.9: 4 residues within 4Å: Chain A: R.435, M.454 Chain C: G.6, C.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.435 Water bridges: A:A.277

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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