SMTL ID : 2i7d.1

Structure of Human cytosolic deoxyribonucleotidase in complex with deoxyuridine, AlF4 and Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.8, D.10, D.142, D.143 Ligands: ALF.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.8, A:D.10, A:D.143, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain B: D.8, D.10, D.143 Ligands: ALF.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.8, B:D.10, B:D.143, H2O.15, H2O.15

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 9 residues within 4Å: Chain A: D.8, M.9, D.10, T.97, S.98, K.110, K.132 Ligands: MG.1, DUR.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.8 ALF.5: 9 residues within 4Å: Chain B: D.8, M.9, D.10, T.97, S.98, K.110, K.132 Ligands: MG.4, DUR.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.8

2 x DUR: 2'-DEOXYURIDINE(Non-covalent)

DUR.3: 10 residues within 4Å: Chain A: D.10, F.16, F.42, L.43, A.44, T.97, S.98, P.99, L.100 Ligands: ALF.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.42 Hydrogen bonds: A:D.10, A:F.42, A:A.44, A:T.97, A:K.110 Water bridges: A:E.17, A:R.39, A:R.45, A:R.130 pi-Stacking: A:F.16 DUR.6: 10 residues within 4Å: Chain B: D.10, F.16, F.42, L.43, A.44, T.97, S.98, P.99, L.100 Ligands: ALF.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.42 Hydrogen bonds: B:F.42, B:A.44, B:K.110 Water bridges: B:R.39, B:R.45, B:R.130 pi-Stacking: B:F.16, B:F.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wallden, K. et al., Structures of Human and Murine cytosolic deoxyribonucleotidase: Insights into substrate specificity and catalysis. To be Published

Release Date

2007-10-30

Peptides

5'(3')-deoxyribonucleotidase, cytosolic type: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'(3')-deoxyribonucleotidase, cytosolic type