SMTL ID : 2jaw.1

Crystal structure of D41N variant of human mitochondrial 5'(3')- deoxyribonucleotidase (mdN) in complex with 5-bromovinyldeoxyuridine 5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x BVP: (E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

BVP.1: 17 residues within 4Å: Chain A: N.10, D.12, F.18, F.44, W.45, V.46, S.47, I.62, W.65, F.71, T.99, S.100, P.101, I.102, K.134, D.145 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.18, A:W.45, A:W.65, A:I.102 Hydrogen bonds: A:N.10, A:V.46, A:S.47, A:T.99, A:S.100 Water bridges: A:M.11, A:K.112, A:R.132, A:K.134 Salt bridges: A:K.134 pi-Stacking: A:W.45 BVP.4: 17 residues within 4Å: Chain B: N.10, D.12, F.18, F.44, W.45, V.46, S.47, I.62, W.65, F.71, T.99, S.100, P.101, I.102, K.134, D.145 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.18, B:W.45, B:W.65, B:I.102 Hydrogen bonds: B:N.10, B:D.12, B:V.46, B:S.47, B:S.100 Water bridges: B:M.11, B:K.112, B:R.132, B:K.134 Salt bridges: B:K.134 pi-Stacking: B:W.45

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: A.88, S.89, L.90, T.93 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.88, A:L.90, H2O.3, H2O.3, H2O.4 MG.3: 4 residues within 4Å: Chain A: N.10, D.12, D.145 Ligands: BVP.1 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:D.12, A:D.145, BVP.1, H2O.7, H2O.7 MG.5: 4 residues within 4Å: Chain B: A.88, S.89, L.90, T.93 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.88, B:L.90, H2O.10, H2O.10, H2O.10 MG.6: 4 residues within 4Å: Chain B: N.10, D.12, D.145 Ligands: BVP.4 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:D.12, B:D.145, BVP.4, H2O.14, 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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