SMTL ID : 3ldy.1 (1 other biounit)

An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

2 x DG- DA- DG- DG- DC- DT- DT- DA: DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*A)-3')(Non-covalent)

DG-DA-DG-DG-DC-DT-DT-DA.1: 20 residues within 4Å: Chain A: R.6, Y.35, K.39, P.81, R.82, R.114 Chain B: A.1, T.2, T.3, A.4, A.5, G.6, C.7, C.8, T.9, C.10 Chain C: S.117, I.119 Chain D: A.1 Ligands: DG-DA-DG-DG-DC-DT-DT-DA.5 62 PLIP interactions: 40 interactions with chain A, 22 interactions with chain C Hydrophobic interactions: A:N.36, A:E.40, C:N.36, C:E.40 Hydrogen bonds: A:Y.17, A:G.19, A:S.20, A:S.20, A:S.21, A:N.32, A:N.32, A:N.36, A:N.36, A:K.39, A:N.80, A:Q.87, A:Q.87, A:C.88, A:G.90, A:R.93, A:S.96, A:N.113, A:R.114, C:N.36, C:N.36, C:K.39, C:N.80, C:D.92, C:R.93, C:Y.100, C:Y.100, C:N.113, C:R.114 Water bridges: A:Y.17, A:Q.31, A:V.91, A:V.91, A:V.91, A:D.92, A:R.93, A:R.93, A:R.93, A:R.93, A:Y.100, A:F.110, A:R.114, A:R.114, A:S.117, A:N.118, A:N.118, C:E.40, C:R.93, C:R.93, C:R.114, C:R.114, C:S.117, C:N.118, C:N.118 Salt bridges: A:R.93, A:R.93, C:R.93, C:R.93 DG-DA-DG-DG-DC-DT-DT-DA.5: 20 residues within 4Å: Chain A: S.117, I.119 Chain B: A.1 Chain C: R.6, Y.35, K.39, P.81, R.82, R.114 Chain D: A.1, T.2, T.3, A.4, A.5, G.6, C.7, C.8, T.9, C.10 Ligands: DG-DA-DG-DG-DC-DT-DT-DA.1 Protein-ligand interaction information (PLIP) not available

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.63, C.66, C.109, C.112 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:C.66, A:C.109, A:C.112 ZN.3: 4 residues within 4Å: Chain A: C.4, C.7, C.24, C.27 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4, A:C.7, A:C.24, A:C.27 ZN.6: 4 residues within 4Å: Chain C: C.63, C.66, C.109, C.112 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.63, C:C.66, C:C.109, C:C.112 ZN.7: 4 residues within 4Å: Chain C: C.4, C.7, C.24, C.27 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.4, C:C.7, C:C.24, C:C.27

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.92, R.93, N.113 Chain B: T.2, T.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.92, H2O.1, H2O.1 CA.8: 5 residues within 4Å: Chain C: D.92, R.93, N.113 Chain D: T.2, T.3 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.92, H2O.5, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, B.W. et al., Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI. Structure (2010)

Release Date

2010-04-21

Peptides

restriction endonuclease PacI: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

restriction endonuclease PacI

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