SMTL ID : 8vnr.1

Homing endonuclease H98A I-PpoI-DNA complex at pH6.0 (K+ MES) with 1 mM Mn2+ for 600s and then 100 mM imidazole for 15 hrs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: A.13, G.14 Chain D: N.118 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.97, D:N.118 NA.3: 4 residues within 4Å: Chain B: A.13, G.14 Chain C: A.97, N.118 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.97, C:N.118

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: T.10, T.11 Chain B: G.14, A.15 Chain C: L.115 No protein-ligand interaction detected (PLIP) GOL.4: 5 residues within 4Å: Chain A: G.14, A.15 Chain B: T.10, T.11 Chain D: L.115 No protein-ligand interaction detected (PLIP) GOL.7: 6 residues within 4Å: Chain C: H.26, V.28, C.99, N.101, R.139 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.139 GOL.8: 5 residues within 4Å: Chain C: H.26, E.42, N.101, R.103 Ligands: GOL.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.26, C:E.42, C:N.101, C:R.103 Water bridges: C:R.103 GOL.11: 5 residues within 4Å: Chain D: H.26, V.28, C.99, N.101, R.139 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.139 Water bridges: D:H.100, D:R.139

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain C: C.124, C.131, H.133, C.137 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.124, C:C.131, C:H.133, C:C.137 ZN.6: 4 residues within 4Å: Chain C: C.40, C.99, C.104, H.109 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.40, C:C.99, C:C.104, C:H.109 ZN.9: 4 residues within 4Å: Chain D: C.124, C.131, H.133, C.137 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.124, D:C.131, D:H.133, D:C.137 ZN.10: 4 residues within 4Å: Chain D: C.40, C.99, C.104, H.109 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.40, D:C.99, D:C.104, D:H.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C. et al., Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s. To Be Published

Release Date

2024-07-10

Peptides

Intron-encoded endonuclease I-PpoI: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

Intron-encoded endonuclease I-PpoI

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