SMTL ID : 7a1f.1

Crystal structure of human 5' exonuclease Appollo in complex with 5'dAMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: D.35, H.36, D.120 Ligands: NI.2, D5M.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.35, A:H.36, A:D.120, H2O.2, H2O.2 FE.5: 5 residues within 4Å: Chain B: D.35, H.36, D.120 Ligands: NI.6, D5M.8 6 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:D.35, B:H.36, B:D.120, D5M.8, H2O.12, H2O.12

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 6 residues within 4Å: Chain A: H.31, H.33, H.99, D.120 Ligands: FE.1, D5M.4 6 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.31, A:H.33, A:H.99, A:D.120, H2O.2, D5M.4 NI.6: 6 residues within 4Å: Chain B: H.31, H.33, H.99, D.120 Ligands: FE.5, D5M.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.31, B:H.33, B:H.99, B:D.120, H2O.12

4 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.3: 13 residues within 4Å: Chain A: T.147, Y.182, K.186, T.257, S.258, R.259, Y.273, S.274, D.275, H.276, R.301 Chain B: Q.87 Ligands: D5M.4 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.147 Hydrogen bonds: A:Y.182, A:T.257, A:S.258, A:D.275, A:R.301, A:R.301, B:Q.87 Water bridges: A:K.186, A:K.186, A:R.259, A:K.260, A:H.276 Salt bridges: A:K.186, A:H.276 pi-Cation interactions: A:R.259, A:R.301 D5M.4: 11 residues within 4Å: Chain A: M.1, H.33, S.34, D.35, H.99, D.120, Y.182, H.276 Ligands: FE.1, NI.2, D5M.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.34, A:S.34 Water bridges: A:N.2, A:N.2, A:S.183 Salt bridges: A:H.33, A:H.99, A:H.276 D5M.7: 12 residues within 4Å: Chain B: T.147, Y.182, K.186, T.257, S.258, R.259, Y.273, S.274, D.275, H.276, R.301 Ligands: D5M.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.147 Hydrogen bonds: B:S.258, B:S.258, B:D.275, B:R.301, B:R.301 Water bridges: B:K.186, B:R.259, B:R.259, B:R.259, B:H.276 Salt bridges: B:K.186 pi-Cation interactions: B:R.259, B:R.301 D5M.8: 11 residues within 4Å: Chain B: M.1, H.33, S.34, D.35, H.99, D.120, Y.182, H.276 Ligands: FE.5, NI.6, D5M.7 8 PLIP interactions: 8 interactions with chain B Water bridges: B:N.2, B:N.2, B:N.2, B:S.183, B:S.183 Salt bridges: B:H.33, B:H.99, B:H.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baddock, H.T. et al., A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family. Nucleic Acids Res. (2021)

Release Date

2021-01-20

Peptides

5' exonuclease Apollo: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

5' exonuclease Apollo

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