SMTL ID : 7qqu.1

SpCas9 bound to FANCF off-target2 DNA substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: G.23, U.24 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain A: U.52 No protein-ligand interaction detected (PLIP)

13 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.3: 5 residues within 4Å: Chain A: U.14, G.15, C.16 Chain C: T.16, A.17 No protein-ligand interaction detected (PLIP) K.4: 3 residues within 4Å: Chain A: A.67, U.68 Chain B: T.1102 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.1102, H2O.14 K.5: 2 residues within 4Å: Chain A: A.70 Chain B: Q.1350 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:Q.1350, H2O.1, H2O.3, H2O.16, H2O.21 K.6: 1 residues within 4Å: Chain A: G.29 No protein-ligand interaction detected (PLIP) K.7: 1 residues within 4Å: Chain B: E.57 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.57, H2O.5, H2O.15, H2O.18, H2O.19 K.8: 4 residues within 4Å: Chain B: L.623, T.624, F.626, Y.656 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.623, B:T.624, B:F.626, B:Y.656, H2O.23 K.9: 6 residues within 4Å: Chain B: G.361, Y.362, G.365, G.366, A.367, K.401 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.362, B:G.365, B:A.367, H2O.2 K.10: 2 residues within 4Å: Chain B: A.640, F.643 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.640, B:F.643, H2O.18 K.11: 4 residues within 4Å: Chain B: I.226, L.229, P.230, E.232 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.226, B:L.229, B:E.232, H2O.16 K.12: 2 residues within 4Å: Chain B: E.108, K.111 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.108, H2O.8, H2O.19 K.13: 3 residues within 4Å: Chain B: E.584, R.586, N.588 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.584, B:R.586, H2O.17 K.14: 3 residues within 4Å: Chain B: E.493, T.496, F.498 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.493, B:T.496, H2O.14, H2O.17 K.15: 4 residues within 4Å: Chain A: U.12 Chain C: G.18, G.19, A.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pacesa, M. et al., Structural basis for Cas9 off-target activity. Cell (2022)

Release Date

2022-10-26

Peptides

CRISPR-associated endonuclease Cas9/Csn1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

CRISPR-associated endonuclease Cas9/Csn1

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