SMTL ID : 3e54.1

Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

DG-DG-DT-DA-DG-DC-DC-DA-DA.1: 39 residues within 4Å: Chain A: E.19 Chain B: A.18, E.19, G.20, S.21, F.22, S.23, V.24, S.25, I.26, K.27, F.28, Q.29, R.37, K.67, K.101, T.137, S.140, K.142, G.143, Y.144, R.145, K.146 Chain C: A.13 Chain D: T.1, T.2, G.3, G.4, C.5, T.6, A.7, C.8, C.9, T.10, A.12, A.13 Ligands: MG.3, MG.5, EOH.8 29 PLIP interactions: 19 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:D.31, B:V.32 Hydrogen bonds: B:A.18, B:K.27, B:Q.29, B:F.33, B:R.37, B:R.37, B:N.80, B:F.81, B:N.82, B:E.141, B:K.142, A:E.19, A:E.19, A:Q.46, A:K.47, A:Q.70, A:Q.70 Water bridges: B:R.63, B:A.68, B:Q.70, B:D.79, A:K.47, A:K.47, A:N.48 Salt bridges: B:R.63, B:H.120, A:K.47

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

DG-DA-DG-DA-DG-DT-DC-DA-DG.2: 40 residues within 4Å: Chain A: A.18, E.19, G.20, S.21, F.22, S.23, V.24, S.25, I.26, K.27, F.28, Q.29, R.37, T.45, K.67, K.101, T.137, S.140, K.142, G.143, Y.144, R.145, K.146 Chain B: E.19 Chain C: C.1, T.2, G.3, A.4, C.5, T.6, C.7, T.8, C.9, T.10, A.12, A.13 Chain D: A.13 Ligands: MG.5, MG.7, EOH.10 Protein-ligand interaction information (PLIP) not available

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: E.19, Q.46 Chain B: E.17, A.18 Chain D: A.13 Ligands: DG-DG-DT-DA-DG-DC-DC-DA-DA.1, EOH.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.19, A:E.19, B:A.18 MG.4: 2 residues within 4Å: Chain A: D.39 Chain C: A.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.39, A:D.39 MG.5: 6 residues within 4Å: Chain A: E.19 Chain B: E.19 Chain C: A.13 Chain D: A.13 Ligands: DG-DG-DT-DA-DG-DC-DC-DA-DA.1, DG-DA-DG-DA-DG-DT-DC-DA-DG.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.19, B:E.19 MG.6: 2 residues within 4Å: Chain B: D.39 Chain D: G.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.39, B:D.39 MG.7: 6 residues within 4Å: Chain A: A.18 Chain B: E.19, Q.46 Chain C: A.12, A.13 Ligands: DG-DA-DG-DA-DG-DT-DC-DA-DG.2 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.19, B:E.19, A:A.18

3 x EOH: ETHANOL(Non-functional Binders)

EOH.8: 5 residues within 4Å: Chain B: A.18, K.101 Chain D: A.12 Ligands: DG-DG-DT-DA-DG-DC-DC-DA-DA.1, MG.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.101, B:K.101 EOH.9: 2 residues within 4Å: Chain C: T.11 Chain D: T.11 No protein-ligand interaction detected (PLIP) EOH.10: 4 residues within 4Å: Chain A: A.18, K.101 Chain C: A.12 Ligands: DG-DA-DG-DA-DG-DT-DC-DA-DG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.101, A:K.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomura, N. et al., Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases. Nucleic Acids Res. (2008)

Release Date

2008-12-30

Peptides

RRNA intron-encoded endonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RRNA intron-encoded endonuclease