SMTL ID : 1z4p.1

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with deoxyriboguanosine 5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

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

2 x DGP: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

DGP.2: 14 residues within 4Å: Chain A: N.10, D.12, F.18, F.44, W.45, V.46, S.47, E.48, W.65, F.71, T.99, S.100, K.134 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.18 Hydrogen bonds: A:N.10, A:N.10, A:D.12, A:D.12, A:V.46, A:S.47, A:S.47, A:E.48, A:T.99, A:S.100 Water bridges: A:M.11, A:K.112, A:K.112, A:K.112, A:R.132, A:K.134, A:K.134 Salt bridges: A:K.134 pi-Stacking: A:W.45 DGP.4: 14 residues within 4Å: Chain B: N.10, D.12, F.18, F.44, W.45, V.46, S.47, E.48, W.65, F.71, T.99, S.100, K.134 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.18 Hydrogen bonds: B:N.10, B:N.10, B:D.12, B:D.12, B:V.46, B:S.47, B:S.47, B:E.48, B:S.100 Water bridges: B:M.11, B:K.112, B:K.112, B:K.112, B:R.132, 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., Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase. STRUCTURE (2005)

Release Date

2005-07-26

Peptides

5'(3')-deoxyribonucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

5'(3')-deoxyribonucleotidase

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