SMTL ID : 6fb0.1

Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with its target DNA (Haemoglobin beta subunit gene) in the presence of Calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.19 Chain B: G.18 Chain C: C.14 Chain D: A.15 Ligands: ACT.8 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:G.18, A:D.19, A:D.19, H2O.4, H2O.6 CA.2: 2 residues within 4Å: Chain A: A.133, N.135 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.133, A:N.135, H2O.1, H2O.1, H2O.4 CA.6: 5 residues within 4Å: Chain A: S.18 Chain B: D.19 Chain C: A.15 Chain D: G.14 Ligands: PGO.5 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.19, B:D.19, A:S.18, H2O.1, H2O.2 CA.7: 2 residues within 4Å: Chain B: A.133, N.135 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.133, B:N.135, H2O.2, H2O.4, H2O.4

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: F.53, K.56, E.60 Chain B: K.95 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.56 Hydrophobic interactions: B:K.95 ACT.8: 9 residues within 4Å: Chain A: Q.46, R.50 Chain B: D.17, K.97, Q.100, D.136 Chain D: A.15, G.16 Ligands: CA.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.50, B:K.97 Hydrogen bonds: B:Q.100 ACT.9: 8 residues within 4Å: Chain A: K.95 Chain B: F.8, Y.11, L.12, F.53, K.56, L.57, E.60 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.95, B:K.56 Hydrophobic interactions: B:Y.11, B:F.53 ACT.10: 1 residues within 4Å: Chain B: H.84 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.84 ACT.11: 4 residues within 4Å: Chain B: Y.4, N.5, F.8, E.60 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.60 Hydrogen bonds: B:N.5, B:N.5 Water bridges: B:K.3

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

PGO.4: 6 residues within 4Å: Chain A: D.129, A.132, A.133, S.137, R.140, T.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.137, A:R.140 Water bridges: A:A.132, A:S.137 PGO.5: 11 residues within 4Å: Chain A: D.17, L.96, K.97, Q.100, L.134, N.135, D.136 Chain B: Q.46, R.50 Chain C: G.16 Ligands: CA.6 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.97, A:Q.100 Water bridges: A:D.17, A:D.17, A:S.18, A:S.18, A:D.136, B: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: A
DNA endonuclease I-CreI: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA endonuclease I-CreI

DNA endonuclease I-CreI

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