SMTL ID : 5hlk.1

Crystal structure of the ternary EcoRV-DNA-Lu complex with cleaved DNA substrate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

DA-DA-DA-DG-DA-DT.1: 24 residues within 4Å: Chain A: N.69, G.108, T.110, S.111, F.112, K.118, N.119, T.185 Chain B: S.182, G.183, N.184, T.185, T.221, S.222, R.225, N.230 Ligands: DA-DT-DC-DT-DT.3, DA-DT-DC-DT-DT-DT.4, DA-DT-DC-DT-DT-DT.4, DA-DT-DC-DT-DT-DT.4, DA-DT-DC-DT-DT-DT.4, DA-DT-DC-DT-DT-DT.4, DA-DT-DC-DT-DT-DT.4, NA.10 Protein-ligand interaction information (PLIP) not available DA-DA-DA-DG-DA-DT.2: 24 residues within 4Å: Chain A: L.179, S.182, G.183, N.184, Y.218, T.221, S.222, R.225, N.230 Chain B: N.69, G.108, T.110, S.111, F.112, K.118, N.119, T.185 Ligands: DA-DT-DC-DT-DT.3, DA-DT-DC-DT-DT.3, DA-DT-DC-DT-DT.3, DA-DT-DC-DT-DT.3, DA-DT-DC-DT-DT.3, DA-DT-DC-DT-DT-DT.4, NA.17 Protein-ligand interaction information (PLIP) not available

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

DA-DT-DC-DT-DT.3: 26 residues within 4Å: Chain A: T.36, E.44, I.90, K.91, T.92, T.93, Y.94, T.105, G.181, S.182, T.185, N.187 Chain B: K.37, Q.67, Q.68, N.69 Ligands: DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.2, DA-DA-DA-DG-DA-DT.2, DA-DA-DA-DG-DA-DT.2, DA-DA-DA-DG-DA-DT.2, DA-DA-DA-DG-DA-DT.2, DA-DA-DA-DG-DA-DT.2, DA-DT-DC-DT-DT-DT.4, EDO.8, LU.11 Protein-ligand interaction information (PLIP) not available DA-DT-DC-DT-DT.4: 28 residues within 4Å: Chain A: K.37, Q.67, Q.68, N.69 Chain B: T.36, E.44, D.73, K.91, T.92, T.93, Y.94, T.105, R.139, G.181, S.182, T.185, N.187 Ligands: DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.2, DA-DT-DC-DT-DT.3, LU.12, LU.18, LU.19 Protein-ligand interaction information (PLIP) not available

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

EDO.5: 5 residues within 4Å: Chain A: N.99, K.166, H.194, Y.195, K.196 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.195, A:K.196 Water bridges: A:N.99, A:K.166 EDO.6: 2 residues within 4Å: Chain A: D.209, E.210 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.235 EDO.7: 8 residues within 4Å: Chain A: N.14, Y.17, D.18, V.19, F.43, F.46, V.165 Ligands: NA.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.14, A:V.19 EDO.8: 8 residues within 4Å: Chain A: E.44, D.73, D.89, I.90, K.91 Chain B: K.37 Ligands: DA-DT-DC-DT-DT.3, LU.11 No protein-ligand interaction detected (PLIP) EDO.13: 8 residues within 4Å: Chain B: N.14, Y.17, D.18, V.19, F.46, Y.162, V.165 Ligands: NA.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.19 Water bridges: B:N.14, B:D.18 EDO.14: 4 residues within 4Å: Chain B: Y.109, G.183, T.186, R.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.220 Water bridges: B:R.225 EDO.15: 4 residues within 4Å: Chain B: D.206, S.207, D.209, E.210 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.207 Water bridges: B:D.209, B:D.209

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

NA.9: 4 residues within 4Å: Chain A: N.14, Y.17, D.18 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.17 NA.10: 5 residues within 4Å: Chain A: G.108, T.185, T.186 Ligands: DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.185 NA.16: 4 residues within 4Å: Chain B: N.14, Y.17, D.18 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.17 NA.17: 5 residues within 4Å: Chain B: G.108, T.185, T.186 Ligands: DA-DA-DA-DG-DA-DT.2, DA-DA-DA-DG-DA-DT.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.186, B:T.186

4 x LU: LUTETIUM (III) ION(Non-covalent)

LU.11: 4 residues within 4Å: Chain A: E.44, D.73 Ligands: DA-DT-DC-DT-DT.3, EDO.8 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.44, A:E.44, A:D.73, H2O.1, H2O.1 LU.12: 6 residues within 4Å: Chain A: K.37 Chain B: E.44, D.73 Ligands: DA-DT-DC-DT-DT-DT.4, LU.18, LU.19 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.44, B:D.73, B:D.73 LU.18: 4 residues within 4Å: Chain B: E.44, D.73 Ligands: DA-DT-DC-DT-DT-DT.4, LU.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.44, B:E.44, B:D.73, H2O.2, H2O.5 LU.19: 5 residues within 4Å: Chain B: D.73, D.89, I.90 Ligands: DA-DT-DC-DT-DT-DT.4, LU.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sinha, K. et al., Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex. Biochemistry (2016)

Release Date

2016-11-09

Peptides

Type-2 restriction enzyme EcoRV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Type-2 restriction enzyme EcoRV

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