SMTL ID : 1z4m.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: N.10, D.12, D.144, D.145 Ligands: U5P.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.12, A:D.145, H2O.2, H2O.2 MG.4: 5 residues within 4Å: Chain B: N.10, D.12, D.144, D.145 Ligands: U5P.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.12, B:D.145, H2O.9, H2O.9

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.2: 18 residues within 4Å: Chain A: N.10, M.11, D.12, F.18, F.44, W.45, V.46, S.47, W.65, F.71, T.99, S.100, P.101, I.102, K.112, K.134 Ligands: MG.1, GOL.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.10, A:M.11, A:D.12, A:S.47, A:T.99, A:T.99, A:S.100 Water bridges: A:S.47, A:I.102, A:K.112, A:K.112, A:R.132, A:R.132, A:K.134, A:K.134 Salt bridges: A:K.112, A:K.134 pi-Stacking: A:W.45 U5P.5: 18 residues within 4Å: Chain B: N.10, M.11, D.12, F.18, F.44, W.45, V.46, S.47, W.65, F.71, T.99, S.100, P.101, I.102, K.112, K.134 Ligands: MG.4, GOL.6 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.10, B:M.11, B:D.12, B:D.12, B:S.47, B:T.99, B:S.100 Water bridges: B:S.47, B:I.102, B:K.112, B:K.112, B:R.132, B:R.132, B:K.134, B:K.134 Salt bridges: B:K.112, B:K.134 pi-Stacking: B:W.45

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: I.62, W.65, E.66, I.102, K.103, M.104 Ligands: U5P.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.66, A:K.103, A:M.104 Water bridges: A:R.132 GOL.6: 7 residues within 4Å: Chain B: I.62, W.65, E.66, I.102, K.103, M.104 Ligands: U5P.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.66, B:E.66, B:K.103, B:M.104 Water bridges: B:R.132

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
A

B
A

5'(3')-deoxyribonucleotidase

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