SMTL ID : 1z4j.1

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 2'-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: 4 residues within 4Å: Chain A: N.10, D.12, D.145 Ligands: U2P.3 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.12, A:D.145, H2O.1, H2O.1, U2P.3 MG.2: 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.6, H2O.6, H2O.6 MG.5: 4 residues within 4Å: Chain B: N.10, D.12, D.145 Ligands: U2P.7 5 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.12, B:D.145, H2O.7, H2O.7, U2P.7 MG.6: 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

2 x U2P: PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER(Non-covalent)

U2P.3: 16 residues within 4Å: Chain A: N.10, M.11, D.12, F.18, F.44, W.45, V.46, T.99, S.100, P.101, I.102, K.112, R.132, K.134, D.145 Ligands: MG.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:W.45 Hydrogen bonds: A:N.10, A:M.11, A:D.12, A:D.12, A:V.46, A:T.99, A:T.99, A:S.100, A:R.132 Water bridges: A:E.19, A:R.41, A:F.44, A:S.47, A:S.100, A:S.100, A:S.100, A:S.100, A:I.102, A:K.112, A:K.134, A:K.134, A:D.145, A:R.146 Salt bridges: A:K.112, A:K.134 pi-Stacking: A:F.18 U2P.7: 16 residues within 4Å: Chain B: N.10, M.11, D.12, F.18, F.44, W.45, V.46, T.99, S.100, P.101, I.102, K.112, R.132, K.134, D.145 Ligands: MG.5 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:W.45 Hydrogen bonds: B:N.10, B:M.11, B:D.12, B:D.12, B:D.12, B:V.46, B:T.99, B:S.100, B:R.132 Water bridges: B:E.19, B:R.41, B:F.44, B:S.47, B:S.100, B:S.100, B:S.100, B:S.100, B:I.102, B:K.112, B:K.134, B:K.134, B:D.145, B:R.146 Salt bridges: B:K.112, B:K.134 pi-Stacking: B:F.18

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: I.62, E.66, M.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.66 GOL.8: 3 residues within 4Å: Chain B: I.62, E.66, M.104 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.66 Water bridges: B:E.66

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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