SMTL ID : 6ozo.1

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 30 min soak in 10 mM Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.52, D.126, D.240 Chain C: U.12 Ligands: MN.11 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.52, A:D.240, H2O.2, H2O.6, H2O.7 MN.2: 3 residues within 4Å: Chain A: L.45, Q.46, Y.72 No protein-ligand interaction detected (PLIP) MN.7: 4 residues within 4Å: Chain B: D.52, D.240 Chain D: U.12 Ligands: MN.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.52, B:D.240, H2O.5, H2O.7, H2O.7 MN.8: 5 residues within 4Å: Chain B: D.52, D.126 Chain D: A.11, U.12 Ligands: MN.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.52, B:D.126, H2O.4, H2O.6 MN.9: 4 residues within 4Å: Chain B: L.45, Q.46, Y.72, P.73 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.72, H2O.5, H2O.5 MN.11: 5 residues within 4Å: Chain A: D.52, D.126 Chain C: A.11, U.12 Ligands: MN.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.52, A:D.126, H2O.1, H2O.1 MN.12: 2 residues within 4Å: Chain C: U.12, A.13 No protein-ligand interaction detected (PLIP) MN.13: 1 residues within 4Å: Chain C: U.18 No protein-ligand interaction detected (PLIP) MN.14: 2 residues within 4Å: Chain D: U.12, A.13 No protein-ligand interaction detected (PLIP) MN.15: 1 residues within 4Å: Chain D: U.18 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: R.38 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.31 GOL.4: 3 residues within 4Å: Chain A: E.106, Q.109, E.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.113

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

EDO.5: 1 residues within 4Å: Chain A: H.202 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain B: D.201, H.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.201

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

PGE.6: 5 residues within 4Å: Chain A: P.73, H.225, H.226, C.228, R.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.229

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

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