SMTL ID : 6ozq.1

Crystal structure of Mus musculus (Mm) Endonuclease V (K155M) in complex with a 23mer RNA oligo containing an inosine after a 100 min soak in 10 mM Mn2+ and K+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.52, D.126, D.240 Chain C: U.12 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.52, A:D.126, A:D.240, H2O.1, H2O.1 MN.6: 4 residues within 4Å: Chain B: D.52, D.126, D.240 Chain D: U.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.52, B:D.126, B:D.240, H2O.3, H2O.4 MN.9: 2 residues within 4Å: Chain C: A.17, U.18 No protein-ligand interaction detected (PLIP) MN.10: 1 residues within 4Å: Chain C: A.13 No protein-ligand interaction detected (PLIP) MN.11: 2 residues within 4Å: Chain D: A.17, U.18 No protein-ligand interaction detected (PLIP) MN.12: 2 residues within 4Å: Chain B: R.244 Chain D: A.13 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: F.42, S.43, G.44, L.45, Q.46, Y.72 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.44, A:L.45, A:Q.46 Water bridges: A:F.42 GOL.3: 4 residues within 4Å: Chain A: D.39, P.40, S.41, S.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.43 GOL.7: 6 residues within 4Å: Chain B: F.42, S.43, G.44, L.45, Q.46, Y.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.44, B:L.45

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

EDO.4: 2 residues within 4Å: Chain A: D.201, H.202 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain B: D.201, H.202 No protein-ligand interaction detected (PLIP)

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

PGE.5: 4 residues within 4Å: Chain A: L.75, H.225, H.226, C.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.226

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