SMTL ID : 1fiu.1

TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x DT- DG- DC- DG: DNA (5'-D(*TP*GP*CP*G)-3')(Non-covalent)

DT-DG-DC-DG.1: 12 residues within 4Å: Chain A: D.34, S.36, R.191, S.192, R.227 Chain B: Q.63, S.99 Ligands: DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.4, DC-DC-DG-DG-DC-DG-DC.4, DC-DC-DG-DG-DC-DG-DC.4, DC-DC-DG-DG-DC-DG-DC.4 Protein-ligand interaction information (PLIP) not available DT-DG-DC-DG.3: 14 residues within 4Å: Chain A: Q.63, S.99 Chain B: D.34, S.36, T.38, R.39, R.191, S.192, R.227 Ligands: DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.4 Protein-ligand interaction information (PLIP) not available DT-DG-DC-DG.5: 12 residues within 4Å: Chain C: Q.63 Chain D: N.37, R.39, R.191, S.192, S.226, R.227 Ligands: DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.8, DC-DC-DG-DG-DC-DG-DC.8, DC-DC-DG-DG-DC-DG-DC.8, DC-DC-DG-DG-DC-DG-DC.8 Protein-ligand interaction information (PLIP) not available DT-DG-DC-DG.7: 16 residues within 4Å: Chain C: D.34, S.36, N.37, T.38, R.191, S.192, S.226, R.227 Chain D: Q.63, S.99, R.102 Ligands: DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.8 Protein-ligand interaction information (PLIP) not available

4 x DC- DC- DG- DG- DC- DG- DC: DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')(Non-covalent)

DC-DC-DG-DG-DC-DG-DC.2: 35 residues within 4Å: Chain A: P.61, Q.63, T.64, N.67, R.100, R.191, D.193 Chain B: S.31, D.34, S.36, R.59, G.62, Q.63, S.65, G.66, D.140, K.187, W.188, T.189, R.191, R.194, N.197, R.227 Ligands: DT-DG-DC-DG.1, DT-DG-DC-DG.3, DT-DG-DC-DG.3, DT-DG-DC-DG.3, DT-DG-DC-DG.3, DC-DC-DG-DG-DC-DG-DC.4, DC-DC-DG-DG-DC-DG-DC.4, DC-DC-DG-DG-DC-DG-DC.4, DC-DC-DG-DG-DC-DG-DC.4, MG.9, MG.15, ACY.16 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG-DC-DG-DC.4: 34 residues within 4Å: Chain A: S.31, D.34, S.36, R.59, G.62, Q.63, S.65, G.66, D.140, K.187, W.188, T.189, R.191, R.194, N.197, R.227 Chain B: P.61, Q.63, T.64, N.67, R.191, D.193 Ligands: DT-DG-DC-DG.1, DT-DG-DC-DG.1, DT-DG-DC-DG.1, DT-DG-DC-DG.1, DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.2, DC-DC-DG-DG-DC-DG-DC.2, DT-DG-DC-DG.3, MG.10, MG.13, ACY.14 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG-DC-DG-DC.6: 34 residues within 4Å: Chain C: S.31, D.34, S.36, R.59, G.62, Q.63, S.65, G.66, D.140, K.187, W.188, T.189, R.191, R.194, N.197, R.227 Chain D: P.61, Q.63, T.64, N.67, R.191, D.193 Ligands: DT-DG-DC-DG.5, DT-DG-DC-DG.7, DT-DG-DC-DG.7, DT-DG-DC-DG.7, DT-DG-DC-DG.7, DC-DC-DG-DG-DC-DG-DC.8, DC-DC-DG-DG-DC-DG-DC.8, DC-DC-DG-DG-DC-DG-DC.8, DC-DC-DG-DG-DC-DG-DC.8, MG.11, MG.17, ACY.18 Protein-ligand interaction information (PLIP) not available DC-DC-DG-DG-DC-DG-DC.8: 35 residues within 4Å: Chain C: P.61, Q.63, T.64, N.67, R.191, D.193 Chain D: S.31, D.34, S.36, R.59, G.62, Q.63, S.65, G.66, E.70, D.140, K.187, W.188, T.189, R.191, R.194, N.197, R.227 Ligands: DT-DG-DC-DG.5, DT-DG-DC-DG.5, DT-DG-DC-DG.5, DT-DG-DC-DG.5, DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.6, DC-DC-DG-DG-DC-DG-DC.6, DT-DG-DC-DG.7, MG.12, MG.19, ACY.20 Protein-ligand interaction information (PLIP) not available

8 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain B: D.140 Ligands: DC-DC-DG-DG-DC-DG-DC.2, MG.15, ACY.16 5 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.140, H2O.1, H2O.18, H2O.21, ACY.16 MG.10: 4 residues within 4Å: Chain A: D.140 Ligands: DC-DC-DG-DG-DC-DG-DC.4, MG.13, ACY.14 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.140, H2O.2, H2O.8, H2O.9 MG.11: 4 residues within 4Å: Chain C: D.140 Ligands: DC-DC-DG-DG-DC-DG-DC.6, MG.17, ACY.18 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.140, H2O.5, H2O.28, H2O.28 MG.12: 4 residues within 4Å: Chain D: D.140 Ligands: DC-DC-DG-DG-DC-DG-DC.8, MG.19, ACY.20 5 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: D:D.140, ACY.20, H2O.39, H2O.42, H2O.43 MG.13: 5 residues within 4Å: Chain A: D.140, C.186 Ligands: DC-DC-DG-DG-DC-DG-DC.4, MG.10, ACY.14 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.140, A:C.186, H2O.3, H2O.8, ACY.14 MG.15: 5 residues within 4Å: Chain B: D.140, C.186 Ligands: DC-DC-DG-DG-DC-DG-DC.2, MG.9, ACY.16 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.140, B:C.186, H2O.1, H2O.20 MG.17: 5 residues within 4Å: Chain C: D.140, C.186 Ligands: DC-DC-DG-DG-DC-DG-DC.6, MG.11, ACY.18 5 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:D.140, C:C.186, H2O.5, H2O.28, ACY.18 MG.19: 5 residues within 4Å: Chain D: D.140, C.186 Ligands: DC-DC-DG-DG-DC-DG-DC.8, MG.12, ACY.20 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.140, D:C.186, H2O.7, H2O.39

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.14: 10 residues within 4Å: Chain A: D.140, S.185, C.186, K.187, N.197, A.198, E.201 Ligands: DC-DC-DG-DG-DC-DG-DC.4, MG.10, MG.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.198 Hydrogen bonds: A:C.186 Water bridges: A:K.187, A:N.197 Salt bridges: A:K.187 ACY.16: 10 residues within 4Å: Chain B: D.140, S.185, C.186, K.187, N.197, A.198, E.201 Ligands: DC-DC-DG-DG-DC-DG-DC.2, MG.9, MG.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.198 Hydrogen bonds: B:C.186 Water bridges: B:K.187 Salt bridges: B:K.187 ACY.18: 10 residues within 4Å: Chain C: D.140, S.185, C.186, K.187, N.197, A.198, E.201 Ligands: DC-DC-DG-DG-DC-DG-DC.6, MG.11, MG.17 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.198 Hydrogen bonds: C:C.186 Water bridges: C:K.187 Salt bridges: C:K.187 ACY.20: 10 residues within 4Å: Chain D: D.140, S.185, C.186, K.187, N.197, A.198, E.201 Ligands: DC-DC-DG-DG-DC-DG-DC.8, MG.12, MG.19 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.198 Hydrogen bonds: D:C.186 Water bridges: D:D.140, D:K.187 Salt bridges: D:K.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deibert, M. et al., Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat.Struct.Biol. (2000)

Release Date

2001-02-07

Peptides

TYPE II RESTRICTION ENZYME NGOMI: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

TYPE II RESTRICTION ENZYME NGOMI

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