SMTL ID : 2jau.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: A.88, 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.4, H2O.4, H2O.4 MG.4: 6 residues within 4Å: Chain A: N.10, D.12, D.144, D.145 Ligands: PO4.2, ATM.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.12, A:D.145, H2O.6, H2O.6 MG.5: 3 residues within 4Å: Chain B: A.88, 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.12, H2O.12, H2O.12 MG.8: 6 residues within 4Å: Chain B: N.10, D.12, D.144, D.145 Ligands: PO4.6, ATM.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.12, B:D.145, H2O.14, H2O.14

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 9 residues within 4Å: Chain A: N.10, M.11, D.12, T.99, S.100, K.112, K.134 Ligands: ATM.3, MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.10, A:N.10, A:M.11, A:D.12, A:T.99, A:T.99, A:S.100, A:S.100 Water bridges: A:K.112, A:K.134 Salt bridges: A:K.112, A:K.134 PO4.6: 9 residues within 4Å: Chain B: N.10, M.11, D.12, T.99, S.100, K.112, K.134 Ligands: ATM.7, MG.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.10, B:N.10, B:M.11, B:D.12, B:D.12, B:T.99, B:S.100, B:S.100 Water bridges: B:K.112, B:K.134 Salt bridges: B:K.112, B:K.134

2 x ATM: 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE(Non-covalent)

ATM.3: 18 residues within 4Å: Chain A: N.10, D.12, F.18, F.44, W.45, V.46, S.47, W.65, F.71, T.99, S.100, P.101, I.102, C.108, K.112, K.134 Ligands: PO4.2, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.18, A:F.18, A:V.46, A:I.102 Hydrogen bonds: A:N.10, A:N.10, A:V.46, A:S.47, A:S.100, A:I.102, A:K.112 Water bridges: A:M.11, A:S.47, A:S.47, A:T.99, A:K.134, A:K.134 Salt bridges: A:K.134 pi-Stacking: A:W.45 ATM.7: 18 residues within 4Å: Chain B: N.10, D.12, F.18, F.44, W.45, V.46, S.47, W.65, F.71, T.99, S.100, P.101, I.102, C.108, K.112, K.134 Ligands: PO4.6, MG.8 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.18, B:F.18, B:V.46, B:I.102 Hydrogen bonds: B:N.10, B:N.10, B:D.12, B:V.46, B:S.47, B:S.100, B:S.100, B:I.102, B:K.112 Water bridges: B:M.11, B:M.11, B:S.47, B:S.47, B:K.134, B:K.134 Salt bridges: B:K.134 pi-Stacking: B:W.45

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

2007-12-11

Peptides

5'(3')-DEOXYRIBONUCLEOTIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'(3')-DEOXYRIBONUCLEOTIDASE

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