SMTL ID : 6ozs.1

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 90 min soak in 10 mM Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 6 residues within 4Å: Chain A: D.47, D.121, D.235 Chain D: U.1 Ligands: MG.10, MG.15 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.47, A:D.235, H2O.1, H2O.1 MG.10: 6 residues within 4Å: Chain A: D.47, V.48, D.121 Chain C: A.11 Chain D: U.1 Ligands: MG.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.47, A:D.121, H2O.1, H2O.2 MG.11: 4 residues within 4Å: Chain B: D.47, D.121, D.235 Chain F: U.1 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.47, B:D.235, H2O.2 MG.14: 5 residues within 4Å: Chain B: D.47, E.95, D.121 Chain E: A.11 Chain F: U.1 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.47, B:D.121, H2O.1 MG.15: 4 residues within 4Å: Chain A: D.235 Chain D: U.1, A.2 Ligands: MG.1 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain F: U.1, A.2 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 4 residues within 4Å: Chain A: D.27, E.29, A.30, R.33 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.33, A:R.33 PGE.12: 3 residues within 4Å: Chain B: H.220, H.221, C.223 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.221

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.3: 4 residues within 4Å: Chain A: G.39, Q.41, K.42, D.112 No protein-ligand interaction detected (PLIP) P6G.4: 3 residues within 4Å: Chain A: K.20, V.23, R.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.20

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: H.220, H.221, C.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.220, A:H.221 GOL.6: 4 residues within 4Å: Chain A: Y.74, E.75, D.76, K.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.74, A:R.105, A:K.109

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain A: L.40, Q.41, Y.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.41, A:Y.67 NA.13: 4 residues within 4Å: Chain B: L.40, Q.41, Y.67, P.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.41, B:Y.67

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 4 residues within 4Å: Chain A: V.72, V.73, E.75, R.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.73, A:E.75, A:E.75, A:R.237 EDO.17: 3 residues within 4Å: Chain F: U.7, G.8, C.9 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 1 residues within 4Å: Chain A: E.166 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, J. et al., Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol.Cell (2019)

Release Date

2019-09-04

Peptides

Endonuclease V: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Endonuclease V