SMTL ID : 3m7k.1

Crystal structure of PacI-DNA Enzyme product complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

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

DT-DA-DA-DG-DC-DC-DT-DC.1: 32 residues within 4Å: Chain A: Y.17, G.19, S.20, S.21, M.28, N.32, N.36, K.39, E.40, N.80, P.81, R.82, Y.84, H.85, I.86, Q.87, C.88, G.90, R.93, Y.100, F.110, N.113 Chain B: G.1, A.2, G.3, G.4, C.5, T.6, T.7 Chain D: T.10 Ligands: PT.5, NA.17 23 PLIP interactions: 7 interactions with chain C, 16 interactions with chain A Hydrogen bonds: C:R.114, C:S.117, A:Q.31, A:K.39, A:K.39, A:R.82, A:R.114, A:R.114 Water bridges: C:R.114, C:R.114, C:R.114, C:R.114, C:R.114, A:R.78, A:T.79, A:R.114, A:R.114 Hydrophobic interactions: A:Y.35, A:K.39 Salt bridges: A:R.6, A:R.6 pi-Stacking: A:Y.35 pi-Cation interactions: A:R.114 DT-DA-DA-DG-DC-DC-DT-DC.18: 32 residues within 4Å: Chain B: T.10 Chain C: Y.17, G.19, S.20, S.21, M.28, N.32, N.36, K.39, E.40, N.80, P.81, R.82, Y.84, H.85, I.86, Q.87, C.88, G.90, R.93, Y.100, F.110, N.113 Chain D: G.1, A.2, G.3, G.4, C.5, T.6, T.7 Ligands: PT.22, NA.34 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.19: 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.20: 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 MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.92, R.93, N.113 Chain D: T.10 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.92, H2O.1, H2O.1, H2O.5 MG.21: 4 residues within 4Å: Chain B: T.10 Chain C: D.92, R.93, N.113 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.92, H2O.5, H2O.5, H2O.9

2 x PT: PLATINUM (II) ION(Non-covalent)

PT.5: 4 residues within 4Å: Chain A: S.21, M.23, M.28 Ligands: DT-DA-DA-DG-DC-DC-DT-DC.1 No protein-ligand interaction detected (PLIP) PT.22: 4 residues within 4Å: Chain C: S.21, M.23, M.28 Ligands: DT-DA-DA-DG-DC-DC-DT-DC.18 No protein-ligand interaction detected (PLIP)

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

NA.6: 2 residues within 4Å: Chain A: H.77, R.78 Ligand excluded by PLIP NA.7: 6 residues within 4Å: Chain A: Q.60, R.61, H.62, L.107 Ligands: SO4.14, SO4.15 Ligand excluded by PLIP NA.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.9: 2 residues within 4Å: Chain A: A.12, D.14 Ligand excluded by PLIP NA.10: 2 residues within 4Å: Chain A: H.77, H.85 Ligand excluded by PLIP NA.11: 2 residues within 4Å: Chain A: K.134 Chain C: E.124 Ligand excluded by PLIP NA.12: 3 residues within 4Å: Chain A: V.127, E.130 Ligands: NA.29 Ligand excluded by PLIP NA.16: 2 residues within 4Å: Chain D: A.8, A.9 Ligand excluded by PLIP NA.17: 3 residues within 4Å: Chain A: T.29, L.33 Ligands: DT-DA-DA-DG-DC-DC-DT-DC.1 Ligand excluded by PLIP NA.23: 2 residues within 4Å: Chain C: H.77, R.78 Ligand excluded by PLIP NA.24: 6 residues within 4Å: Chain C: Q.60, R.61, H.62, L.107 Ligands: SO4.31, SO4.32 Ligand excluded by PLIP NA.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.26: 2 residues within 4Å: Chain C: A.12, D.14 Ligand excluded by PLIP NA.27: 2 residues within 4Å: Chain C: H.77, H.85 Ligand excluded by PLIP NA.28: 2 residues within 4Å: Chain A: E.124 Chain C: K.134 Ligand excluded by PLIP NA.29: 3 residues within 4Å: Chain C: V.127, E.130 Ligands: NA.12 Ligand excluded by PLIP NA.33: 2 residues within 4Å: Chain B: A.8, A.9 Ligand excluded by PLIP NA.34: 3 residues within 4Å: Chain C: T.29, L.33 Ligands: DT-DA-DA-DG-DC-DC-DT-DC.18 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 6 residues within 4Å: Chain A: N.118, I.119, F.120, S.121, E.124 Chain C: R.139 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.120 EDO.30: 6 residues within 4Å: Chain A: R.139 Chain C: N.118, I.119, F.120, S.121, E.124 1 PLIP interactions: 1 interactions with chain C Water bridges: C:F.120

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.14: 3 residues within 4Å: Chain A: H.62, G.64 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.62, A:H.62 SO4.15: 7 residues within 4Å: Chain A: W.54, Y.55, G.56, Q.60, R.61, L.107 Ligands: NA.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.57 SO4.31: 3 residues within 4Å: Chain C: H.62, G.64 Ligands: NA.24 2 PLIP interactions: 2 interactions with chain C Water bridges: C:H.62, C:H.62 SO4.32: 7 residues within 4Å: Chain C: W.54, Y.55, G.56, Q.60, R.61, L.107 Ligands: NA.24 1 PLIP interactions: 1 interactions with chain C Water bridges: C:L.57

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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