SMTL ID : 3c0w.1

I-SceI in complex with a bottom nicked DNA substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x DC- DC- DC- DT- DA- DG- DC- DG- DT: DNA (5'-D(P*DCP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DT)-3')(Non-covalent)

DC-DC-DC-DT-DA-DG-DC-DG-DT.1: 23 residues within 4Å: Chain A: A.1, C.2, G.3, C.4, T.5, A.6, G.7, G.8, G.9, A.13 Chain B: T.15 Chain C: D.44, D.144, D.145, Y.151, N.152, N.163, Q.165, N.192, Y.222, K.223 Ligands: CA.3, NA.4 34 PLIP interactions: 34 interactions with chain C Hydrophobic interactions: C:Y.46, C:Y.46, C:K.63, C:W.149 Hydrogen bonds: C:D.44, C:E.61, C:E.61, C:K.63, C:N.90, C:N.94, C:N.152, C:N.157, C:N.192, C:K.193 Water bridges: C:D.44, C:D.44, C:Q.59, C:Q.59, C:E.61, C:E.61, C:E.61, C:R.88, C:T.98, C:D.144, C:D.145, C:D.145, C:D.145, C:W.149, C:D.150, C:S.166, C:S.166 Salt bridges: C:K.63, C:K.190 pi-Cation interactions: C:K.193

3 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: C.14 Chain B: A.14, T.15 No protein-ligand interaction detected (PLIP) CA.3: 5 residues within 4Å: Chain A: A.13 Chain C: D.44, D.144 Ligands: DC-DC-DC-DT-DA-DG-DC-DG-DT.1, NA.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.44, C:D.144, H2O.4 CA.5: 5 residues within 4Å: Chain A: C.14 Chain C: L.42, G.43, D.145 Ligands: NA.4 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:G.43, C:D.145, H2O.1, H2O.1, H2O.3

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

NA.4: 8 residues within 4Å: Chain A: A.13, C.14 Chain B: T.15 Chain C: D.44, D.145 Ligands: DC-DC-DC-DT-DA-DG-DC-DG-DT.1, CA.3, CA.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moure, C.M. et al., Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway. Nucleic Acids Res. (2008)

Release Date

2008-05-06

Peptides

Intron-encoded endonuclease I-SceI: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

Intron-encoded endonuclease I-SceI

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