SMTL ID : 6fb8.1

Crystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with an altered version of its target DNA at 5NNN region in the presence of Magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: C.14 Chain B: G.15 Chain C: D.19 Chain D: G.18 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:G.18, C:D.19, C:D.19, H2O.1, H2O.3 MG.2: 4 residues within 4Å: Chain A: G.15 Chain B: C.14 Chain C: G.18 Chain D: D.19 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.19, C:G.18, H2O.1, H2O.2 MG.5: 2 residues within 4Å: Chain C: A.133, N.135 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:A.133, H2O.2, H2O.2, H2O.3, H2O.3 MG.8: 2 residues within 4Å: Chain D: A.133, N.135 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:A.133, H2O.3, H2O.3, H2O.3, H2O.4

4 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.3: 5 residues within 4Å: Chain C: F.53, K.56, L.57, E.60 Chain D: K.95 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.57 Hydrogen bonds: C:E.60 PGO.4: 8 residues within 4Å: Chain A: C.16 Chain C: L.96, K.97, Q.100, L.134, N.135, D.136 Chain D: R.50 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.97, C:Q.100 Water bridges: C:D.17, C:G.18, D:Q.46 PGO.6: 6 residues within 4Å: Chain C: K.95 Chain D: F.8, F.53, K.56, L.57, E.60 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.8, D:L.57 Hydrogen bonds: D:E.60, C:K.95 PGO.7: 7 residues within 4Å: Chain B: A.16 Chain C: R.50 Chain D: L.96, K.97, Q.100, L.134, N.135 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:K.97 Hydrogen bonds: D:K.97 Water bridges: D:D.17, D:G.18, D:G.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prieto, J. et al., Understanding the indirect DNA read-out specificity of I-CreI Meganuclease. Sci Rep (2018)

Release Date

2018-07-18

Peptides

DNA endonuclease I-CreI: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

DNA endonuclease I-CreI

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