SMTL ID : 2jar.1

Crystal structure of D12N variant of mouse cytosolic 5'(3')- deoxyribonucleotidase (cdN) in complex with deoxyuridine 5'- monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.1: 14 residues within 4Å: Chain A: N.12, D.14, F.20, F.46, L.47, A.48, N.49, Y.67, T.101, T.102, P.103, L.104, K.136 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.20, A:L.104 Hydrogen bonds: A:N.12, A:A.48, A:N.49, A:Y.67, A:T.102, A:T.102 Water bridges: A:M.13, A:T.102, A:T.102, A:K.114, A:K.136 Salt bridges: A:K.136 UMP.3: 14 residues within 4Å: Chain B: N.12, D.14, F.20, F.46, L.47, A.48, N.49, Y.67, T.101, T.102, P.103, L.104, K.136 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.20, B:L.104 Hydrogen bonds: B:N.12, B:A.48, B:N.49, B:Y.67, B:T.102, B:T.102 Water bridges: B:M.13, B:K.114, B:K.136 Salt bridges: B:K.136

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.12, D.14, D.147 Ligands: UMP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.14, A:D.147, H2O.5, H2O.7 MG.4: 4 residues within 4Å: Chain B: N.12, D.14, D.147 Ligands: UMP.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.14, B:D.147, H2O.12, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wallden, K. et al., Crystal Structures of Human and Murine Deoxyribonucleotidases: Insights Into Recognition of Substrates and Nucleotide Analogues. Biochemistry (2007)

Release Date

2007-11-20

Peptides

5'(3')-DEOXYRIBONUCLEOTIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'(3')-DEOXYRIBONUCLEOTIDASE

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