SMTL ID : 8efg.1

Crystal structure of human TATDN1 bound to dAMP and two zinc ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: N.11, D.221 Ligands: D5M.8 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: A:D.221, A:D.221, H2O.1, D5M.8, D5M.8 ZN.2: 4 residues within 4Å: Chain A: E.111, H.148, H.173 Ligands: D5M.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.111, A:H.148, A:H.173, D5M.8

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: S.234, K.235, I.237 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.237, A:I.237

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: A.271, D.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.271 Water bridges: A:A.271 GOL.5: 5 residues within 4Å: Chain A: I.41, T.239, A.240, F.241, P.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.240 GOL.6: 3 residues within 4Å: Chain A: A.240, F.241, T.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.241, A:T.243 Water bridges: A:F.241 GOL.7: 4 residues within 4Å: Chain A: S.229, S.234, I.237 Ligands: NA.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.234 Water bridges: A:V.227, A:Q.264, A:Q.264

2 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.8: 16 residues within 4Å: Chain A: H.76, E.111, D.117, R.118, H.148, R.150, H.173, S.174, D.176, C.197, D.221 Ligands: ZN.1, ZN.2, D5M.9, 3D1.10, ADE.11 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.174, A:S.174 Water bridges: A:N.11, A:N.11, A:D.117, A:R.118, A:R.118, A:R.150 Salt bridges: A:H.76, A:R.118, A:H.148, A:H.173 pi-Cation interactions: A:R.118 D5M.9: 10 residues within 4Å: Chain A: R.150, C.197, K.200, W.224, C.225, K.228, H.231 Ligands: D5M.8, 3D1.10, ADE.11 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.200, A:C.225 Water bridges: A:R.150, A:K.200, A:G.226 Salt bridges: A:K.200, A:H.231

1 x 3D1: (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol(Non-covalent)

3D1.10: 7 residues within 4Å: Chain A: T.78, R.79, R.118, F.121 Ligands: D5M.8, D5M.9, ADE.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.121 Hydrogen bonds: A:T.78, A:T.78, A:R.79, A:R.118 Water bridges: A:R.79, A:R.79 pi-Stacking: A:F.121, A:F.121

1 x ADE: ADENINE(Non-covalent)

ADE.11: 4 residues within 4Å: Chain A: W.224 Ligands: D5M.8, D5M.9, 3D1.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.118 Water bridges: A:R.118, A:W.224 pi-Stacking: A:W.224, A:W.224, A:W.224, A:W.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dorival, J. et al., Human and bacterial TatD enzymes exhibit apurinic/apyrimidinic (AP) endonuclease activity. Nucleic Acids Res. (2023)

Release Date

2023-02-22

Peptides

Deoxyribonuclease TATDN1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Deoxyribonuclease TATDN1