SMTL ID : 5fbg.2 (1 other biounit)

S1 nuclease from Aspergillus oryzae, mutant D65N, in complex with phosphate, 2'-deoxycytidine and 2'-deoxyguanosine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: W.1, H.6, H.115, D.119 Ligands: ZN.2, PO4.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:W.1, A:H.6, A:D.119 ZN.2: 6 residues within 4Å: Chain A: N.45, H.60, H.115, D.119 Ligands: ZN.1, PO4.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.60, A:H.115, A:D.119 ZN.3: 5 residues within 4Å: Chain A: W.1, H.125, H.148, D.152 Ligands: PO4.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.125, A:H.148, A:D.152, A:D.152, H2O.2

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 6 residues within 4Å: Chain A: F.55, Y.59, N.92, Y.93, I.96, E.105 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.59, A:N.92 NAG.5: 3 residues within 4Å: Chain A: L.224, A.225, N.228 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.228, A:N.228

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

PO4.6: 12 residues within 4Å: Chain A: W.1, H.6, N.45, K.48, H.60, H.115, D.119, H.125, D.152 Ligands: ZN.1, ZN.2, ZN.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.1, A:N.45 Water bridges: A:K.48, A:K.48 Salt bridges: A:K.48, A:H.60, A:H.115, A:H.125

1 x GNG: 2'-DEOXY-GUANOSINE(Non-covalent)

GNG.7: 8 residues within 4Å: Chain A: F.61, D.63, L.124, H.125, A.131, G.132, N.134, H.148 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.131 Hydrogen bonds: A:N.134 Water bridges: A:I.62, A:D.63, A:D.63 Salt bridges: A:D.63 pi-Stacking: A:F.61 pi-Cation interactions: A:F.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koval, T. et al., Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. PLoS ONE (2016)

Release Date

2016-12-28

Peptides

Nuclease S1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Nuclease S1

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