SMTL ID : 6fb9.1

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 Manganese

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: C.14 Chain C: D.19 Chain D: G.18 Chain F: G.1 Ligands: MN.2 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:D.19, D:G.18, H2O.1 MN.2: 10 residues within 4Å: Chain A: C.14 Chain B: C.14 Chain C: G.18, D.19 Chain D: G.18, D.19 Chain E: G.1 Chain F: G.1 Ligands: MN.1, MN.3 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Metal complexes: C:D.19, D:D.19 MN.3: 6 residues within 4Å: Chain B: C.14 Chain C: D.17, G.18 Chain D: D.19 Chain E: G.1 Ligands: MN.2 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:D.19, C:G.18, H2O.1 MN.6: 2 residues within 4Å: Chain C: A.133, N.135 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.133, C:N.135, H2O.1, H2O.1 MN.9: 2 residues within 4Å: Chain D: A.133, N.135 No protein-ligand interaction detected (PLIP)

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

PGO.4: 7 residues within 4Å: Chain C: F.8, Y.11, F.53, K.56, L.57, E.60 Chain D: K.95 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.8, C:Y.11, C:F.53, C:L.57 Hydrogen bonds: C:E.60 PGO.5: 9 residues within 4Å: Chain C: L.96, K.97, Q.100, L.134, N.135, D.136 Chain D: R.50 Chain E: G.1, C.2 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.97, C:Q.100, C:D.136 Water bridges: C:D.17, C:G.18 PGO.7: 6 residues within 4Å: Chain C: K.95 Chain D: F.8, F.53, K.56, L.57, E.60 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.8, D:L.57 Hydrogen bonds: C:K.95 PGO.8: 8 residues within 4Å: Chain C: R.50 Chain D: L.96, K.97, Q.100, L.134, N.135 Chain F: G.1, A.2 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:K.97 Hydrogen bonds: D:K.97, D:D.136 Water bridges: D:D.17, D:N.135, C:Q.46

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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