SMTL ID : 2jao.1

Crystal structure of D12N variant of mouse cytosolic 5'(3')- deoxyribonucleotidase (cdN) in complex with deoxyguanosine 5'- monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: R.5, P.6, V.7, K.196, R.197, S.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.5, A:S.199 Water bridges: A:D.142, A:D.142 GOL.4: 6 residues within 4Å: Chain B: R.5, P.6, V.7, K.196, R.197, S.199 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.5, B:S.199 Water bridges: B:D.142, B:D.142

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

DGP.2: 15 residues within 4Å: Chain A: N.12, D.14, F.20, F.46, L.47, A.48, N.49, Y.67, F.73, T.101, T.102, P.103, L.104, K.136 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.20, A:F.73, A:L.104 Hydrogen bonds: A:N.12, A:D.14, A:A.48, A:N.49, A:N.49, A:Y.67, A:T.102, A:T.102, A:T.102 Water bridges: A:D.14, A:E.21, A:Y.67, A:K.114, A:K.136, A:K.136, A:K.136 Salt bridges: A:K.136 DGP.5: 15 residues within 4Å: Chain B: N.12, D.14, F.20, F.46, L.47, A.48, N.49, Y.67, F.73, T.101, T.102, P.103, L.104, K.136 Ligands: MG.6 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.20, B:F.73, B:L.104 Hydrogen bonds: B:N.12, B:D.14, B:A.48, B:N.49, B:N.49, B:Y.67, B:T.102, B:T.102, B:T.102 Water bridges: B:D.14, B:E.21, B:Y.67, B:K.114, B:K.136, B:K.136, B:K.136 Salt bridges: B:K.136

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: N.12, D.14, D.147 Ligands: DGP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.14, A:D.147, H2O.7, H2O.7 MG.6: 4 residues within 4Å: Chain B: N.12, D.14, D.147 Ligands: DGP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.14, B:D.147, H2O.14, H2O.14

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

2007-11-20

Peptides

5'(3')-DEOXYRIBONUCLEOTIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'(3')-DEOXYRIBONUCLEOTIDASE

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