SMTL ID : 1a73.1

INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x DG- DA- DG- DA- DG- DT- DC- DA: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')(Non-covalent)

DG-DA-DG-DA-DG-DT-DC-DA.1: 25 residues within 4Å: Chain A: A.13 Chain B: T.1, T.2, G.3, A.4, C.5, T.6, C.7, T.8, C.9, T.10 Chain D: N.57, T.60, R.61, Q.63, R.74, G.76, T.79, T.95, A.96, H.98, T.103, W.113, L.116, N.119 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.53, D:N.57, D:K.65, D:K.65, D:T.67, D:K.120, C:N.123 Water bridges: D:Y.50, D:Y.50, D:R.66, D:T.67, D:T.67, D:T.67, D:R.74, D:D.117 Salt bridges: D:R.66 Hydrophobic interactions: C:L.116 DG-DA-DG-DA-DG-DT-DC-DA.2: 25 residues within 4Å: Chain A: T.1, T.2, G.3, A.4, C.5, T.6, C.7, T.8, C.9, T.10 Chain B: A.13 Chain C: N.57, T.60, R.61, Q.63, R.74, G.76, T.79, T.95, A.96, H.98, T.103, W.113, L.116, N.119 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: A.13 Chain C: H.98, N.119 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: A.13 Chain D: H.98, N.119 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain C: C.125, C.132, H.134, C.138 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.125, C:C.132, C:H.134, C:C.138 ZN.5: 4 residues within 4Å: Chain C: C.41, C.100, C.105, H.110 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.41, C:C.100, C:C.105, C:H.110 ZN.6: 4 residues within 4Å: Chain D: C.125, C.132, H.134, C.138 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.125, D:C.132, D:H.134, D:C.138 ZN.7: 4 residues within 4Å: Chain D: C.41, C.100, C.105, H.110 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.41, D:C.100, D:C.105, D:H.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flick, K.E. et al., DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature (1998)

Release Date

1998-10-14

Peptides

INTRON 3 (I-PPO) ENCODED ENDONUCLEASE: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

INTRON 3 (I-PPO) ENCODED ENDONUCLEASE

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