SMTL ID : 6ozm.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: D.32, R.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.32, A:R.38 Water bridges: A:R.38 GOL.2: 5 residues within 4Å: Chain A: Y.79, E.80, D.81, K.114, E.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.80, A:K.114, A:E.115 GOL.13: 5 residues within 4Å: Chain C: G.15 Chain D: A.17, U.18, G.19, C.20 No protein-ligand interaction detected (PLIP)

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

PGE.3: 4 residues within 4Å: Chain A: H.225, H.226, C.228, R.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.229, A:R.229 PGE.6: 5 residues within 4Å: Chain B: P.73, H.225, H.226, C.228, R.229 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.73, B:R.229 Water bridges: B:H.225

3 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.5: 2 residues within 4Å: Chain A: E.106, E.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.113 EDO.10: 3 residues within 4Å: Chain C: A.17, U.18, G.19 No protein-ligand interaction detected (PLIP)

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

MN.7: 4 residues within 4Å: Chain A: D.52, D.240 Chain C: U.12 Ligands: MN.8 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.52, A:D.240, H2O.2, H2O.9, H2O.9 MN.8: 5 residues within 4Å: Chain A: D.52, D.126 Chain C: A.11, U.12 Ligands: MN.7 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.9: 2 residues within 4Å: Chain C: U.12, A.13 No protein-ligand interaction detected (PLIP) MN.11: 5 residues within 4Å: Chain B: D.52, D.126, D.240 Chain D: U.12 Ligands: MN.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.52, B:D.240, H2O.7, H2O.9, H2O.9 MN.12: 5 residues within 4Å: Chain B: D.52, D.126 Chain D: A.11, U.12 Ligands: MN.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.52, B:D.126, H2O.6, H2O.6

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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