SMTL ID : 4aab.1

Crystal structure of the mutant D75N I-CreI in complex with its wild- type target (The four central bases, 2NN region, are composed by GTAC from 5' to 3')

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

5 x PGO: S-1,2-PROPANEDIOL(Non-covalent)(Non-functional Binders)

PGO.1: 9 residues within 4Å: Chain A: R.50 Chain B: D.17, G.18, G.20, K.97, D.136 Chain F: G.1, A.2 Ligands: MG.4 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.136 Hydrogen bonds: B:G.18, B:K.97 Water bridges: B:D.17, A:Q.46 PGO.2: 7 residues within 4Å: Chain B: Q.37, S.39, L.40, S.78, I.80 Chain C: A.3, A.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.37, B:L.38, B:L.40, B:L.40 PGO.5: 6 residues within 4Å: Chain B: K.27, I.76, S.78 Chain C: A.5, A.6, C.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.76 Hydrogen bonds: B:K.27 Water bridges: B:K.27, B:S.39 PGO.6: 6 residues within 4Å: Chain A: K.97, D.136 Chain B: R.50 Chain D: G.1, A.2 Ligands: MG.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.18, A:K.97 PGO.7: 6 residues within 4Å: Chain C: A.13, C.14 Chain D: G.1 Chain E: G.11, T.12, A.13 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 9 residues within 4Å: Chain A: D.19 Chain B: G.18, D.19 Chain C: C.14 Chain D: G.1 Chain E: C.14 Chain F: G.1 Ligands: MG.4, MG.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.19, A:D.19 MG.4: 8 residues within 4Å: Chain A: D.19 Chain B: D.17, G.18 Chain C: A.13, C.14 Chain F: G.1 Ligands: PGO.1, MG.3 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:G.18, A:D.19, H2O.1 MG.8: 7 residues within 4Å: Chain A: G.18, D.19 Chain B: D.19 Chain D: G.1 Chain E: C.14 Ligands: MG.3, PGO.6 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.19, A:G.18, H2O.1

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

NA.9: 4 residues within 4Å: Chain C: G.11, A.13 Chain E: C.14 Chain F: G.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Molina, R. et al., Non-Specific Protein-DNA Interactions Control I-Crei Target Binding and Cleavage. Nucleic Acids Res. (2012)

Release Date

2012-05-02

Peptides

DNA ENDONUCLEASE I-CREI: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA ENDONUCLEASE I-CREI

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