SMTL ID : 6ozl.1

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 2 min soak in Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.52, D.240 Chain C: U.12 Ligands: MN.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.52, A:D.240, H2O.1, H2O.5, H2O.6 MN.2: 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.6: 3 residues within 4Å: Chain B: D.52, D.240 Chain D: U.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.52, B:D.240, H2O.4, H2O.6, H2O.6 MN.7: 4 residues within 4Å: Chain B: D.52, D.126 Chain D: A.11, U.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.52, B:D.126, H2O.4, H2O.4

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: D.32, R.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.38 Water bridges: A:R.38 GOL.9: 3 residues within 4Å: Chain C: A.17, U.18, G.19 No protein-ligand interaction detected (PLIP)

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

PGE.4: 5 residues within 4Å: Chain A: P.73, H.225, H.226, C.228, R.229 No protein-ligand interaction detected (PLIP) PGE.8: 4 residues within 4Å: Chain B: L.75, H.225, H.226, C.228 No protein-ligand interaction detected (PLIP)

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

NA.5: 2 residues within 4Å: Chain A: L.45, Q.46 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.72 Water bridges: A:L.45, A:Q.46

1 x TLA: L(+)-TARTARIC ACID(Non-functional Binders)

TLA.10: 5 residues within 4Å: Chain C: G.15 Chain D: A.17, U.18, G.19, C.20 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

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