SMTL ID : 1mh9.1

Crystal Structure Analysis of deoxyribonucleotidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: D.10, M.11, D.12, T.99, S.100, K.112, K.134 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.10, A:D.10, A:M.11, A:D.12, A:D.12, A:T.99, A:S.100 Water bridges: A:S.100, A:S.100, A:K.112 Salt bridges: A:K.112, A:K.134 PO4.3: 8 residues within 4Å: Chain B: D.10, M.11, D.12, T.99, S.100, K.112, K.134 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.10, B:D.10, B:M.11, B:D.12, B:D.12, B:D.12, B:S.100 Water bridges: B:S.100, B:S.100, B:K.112 Salt bridges: B:K.112, B:K.134

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.10, D.12, D.145 Ligands: PO4.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:D.12, A:D.145, H2O.1, H2O.6 MG.4: 4 residues within 4Å: Chain B: D.10, D.12, D.145 Ligands: PO4.3 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:D.12, B:D.145, H2O.14, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rinaldo-Matthis, A. et al., Crystal structure of a human mitochondrial deoxyribonucleotidase. Nat.Struct.Biol. (2002)

Release Date

2002-10-30

Peptides

deoxyribonucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

deoxyribonucleotidase

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