SMTL ID : 6ozp.1

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 180 min soak in 10 mM Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

11 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 5 residues within 4Å: Chain A: D.45, D.119, D.233 Chain D: U.1 Ligands: MN.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.45, A:D.233, H2O.1, H2O.2 MN.2: 5 residues within 4Å: Chain A: D.45, D.119 Chain C: A.11 Chain D: U.1 Ligands: MN.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.45, A:D.119, H2O.1, H2O.2 MN.3: 2 residues within 4Å: Chain A: L.38, Q.39 No protein-ligand interaction detected (PLIP) MN.12: 4 residues within 4Å: Chain B: D.45, D.233 Chain F: U.1 Ligands: MN.20 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.45, B:D.233, H2O.7, H2O.8 MN.13: 1 residues within 4Å: Chain B: E.238 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.238, H2O.7, H2O.8, H2O.10 MN.14: 2 residues within 4Å: Chain B: L.38, Q.39 No protein-ligand interaction detected (PLIP) MN.20: 5 residues within 4Å: Chain B: D.45, D.119 Chain E: A.11 Chain F: U.1 Ligands: MN.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.45, B:D.119, H2O.7, H2O.7 MN.21: 2 residues within 4Å: Chain D: U.1, A.2 No protein-ligand interaction detected (PLIP) MN.22: 1 residues within 4Å: Chain D: U.7 No protein-ligand interaction detected (PLIP) MN.23: 2 residues within 4Å: Chain F: U.1, A.2 No protein-ligand interaction detected (PLIP) MN.24: 1 residues within 4Å: Chain F: U.7 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: V.70, V.71, E.73, R.235 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.71, A:E.73, A:E.73, A:R.235 Water bridges: A:E.73, A:E.73 GOL.5: 3 residues within 4Å: Chain A: D.32, S.34, S.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.34, A:S.36

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

PG4.6: 5 residues within 4Å: Chain A: K.18, V.21, D.23, V.123 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.18 PG4.15: 4 residues within 4Å: Chain B: D.25, E.27, A.28, R.31 No protein-ligand interaction detected (PLIP)

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

EDO.7: 2 residues within 4Å: Chain A: Y.72, E.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.74 Water bridges: A:E.73, A:R.103 EDO.8: 2 residues within 4Å: Chain A: D.194, H.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.194 EDO.9: 4 residues within 4Å: Chain A: H.125, Q.126, D.154 Ligands: PG4.6 No protein-ligand interaction detected (PLIP) EDO.16: 2 residues within 4Å: Chain B: K.18, V.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.18 EDO.17: 2 residues within 4Å: Chain B: D.194, H.195 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.194, B:D.194 EDO.18: 2 residues within 4Å: Chain B: V.70, V.71 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.73

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

PGE.10: 3 residues within 4Å: Chain A: D.25, A.28, R.31 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.31 PGE.11: 4 residues within 4Å: Chain A: H.218, H.219, C.221, R.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.222 PGE.19: 3 residues within 4Å: Chain B: H.218, H.219, C.221 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